[galaxy-dev] set metadata resubmission
Dear list, I'm just wondering if there is anything special about metadata setting jobs that might lead to problems with job resubmission. For normal jobs resubmission works on our UNIVA cluster, but for setting metadata this seems to be not the case. Best, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Helmholtz-Zentrum für Umweltforschung GmbH - UFZ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 1269, Fax +49 341 235 1468 (optional) max.musterm...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Georg Teutsch Administrative Geschäftsführerin/Administrative Managing Director: Dr. Sabine König ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] Re: galaxy-dev Digest, Vol 155, Issue 3
Dear Jochen, I don't know if its excpected. But at least I can tell that the same is happening here. And I can add if the 000 folder contains 000-999 the pattern repeats in 001. Cheers, Matthias On 21.05.19 17:38, galaxy-dev-requ...@lists.galaxyproject.org wrote: Coming back to my question: this is how an ls -ls looks in my database folder... 2. Apr 14:40 000/ 9. Nov 2015 005/ 19. Nov 2018 007/ 19. Nov 2018 008/ 3. Dez 2015 010/ 10. Jan 2017 012/ 10. Jan 2017 013/ 29. Jun 2017 014/ 4. Jul 2017 015/ 9. Jan 2018 018/ 29. Jun 2017 020/ 21. Sep 2016 021/ 20. Mär 2018 032/ 29. Jan 09:38 033/ 29. Jan 10:32 034/ 16. Jul 2018 035/ 30. Okt 2018 036/ 30. Okt 2018 037/ 30. Okt 2018 038/ 30. Okt 2018 039/ 29. Aug 2018 070/ 29. Aug 2018 071/ 29. Aug 2018 072/ 29. Aug 2018 073/ 29. Aug 2018 074/ 29. Aug 2018 075/ 29. Aug 2018 076/ 29. Aug 2018 077/ 29. Aug 2018 078/ 29. Aug 2018 079/ 29. Aug 2018 080/ 29. Aug 2018 081/ 29. Aug 2018 082/ 29. Aug 2018 083/ 29. Aug 2018 084/ 29. Aug 2018 085/ 29. Aug 2018 086/ 29. Aug 2018 087/ 29. Aug 2018 088/ 29. Aug 2018 089/ 29. Aug 2018 090/ 29. Aug 2018 091/ 29. Aug 2018 092/ 29. Aug 2018 093/ 29. Aug 2018 094/ 29. Aug 2018 095/ 31. Aug 2018 096/ 30. Aug 2018 097/ 1. Sep 2018 098/ 24. Okt 2018 099/ if you look into the 000 folder it restarts: 10. Dez 19:36 100/ 30. Nov 10:45 101/ 10. Dez 19:39 102/ 10. Dez 19:37 103/ 11. Jan 15:13 104/ 11. Jan 11:31 105/ 22. Jan 14:33 106/ 8. Feb 10:46 107/ 14. Feb 15:47 108/ 21. Mär 11:00 109/ 2. Apr 15:22 110/ 21. Mai 17:17 111/ is this the expected behavior? The only thing we did was we archived some of the very early generated datasets. Is this maybe the problem? Cheers Jochen On 14.05.19 15:32, Jochen Bick wrote: Hi, today we found out that some of our files in your galaxy instance are new in "database/files/000/" which is the first folder of your database files. Could some please explain me how galaxy generates new file names? and how this is possible? Thanks in advance Jochen -- ETH Zurich *Jochen Bick* Animal Physiology Institute of Agricultural Sciences Postal address: Universitätstrasse 2 / LFW B 58.1 8092 Zurich, Switzerland Office: Eschikon 27 8315 Lindau, Switzerland Phone +41 52 354 92 06 jochen.b...@usys.ethz.ch <mailto:jochen.b...@usys.ethz.ch> www.ap.ethz.ch -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Helmholtz-Zentrum für Umweltforschung GmbH - UFZ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 1269, Fax +49 341 235 1468 (optional) max.musterm...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Georg Teutsch Administrative Geschäftsführerin/Administrative Managing Director: Dr. Sabine König ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] user login / registration problem
Hi, on our ldap-autoregistration Galaxy-dev instance (details below) no new users can be auto-registered since recently because of https://github.com/galaxyproject/galaxy/issues/7617 to me it seems that the function ``` message, status, user, success = self.__register(trans, **kwd) ``` called in `lib/galaxy/webapps/galaxy/controllers/user.py` (L90) got lost between 19.01 and now. Would be great to get some feedback. I could help with debugging or contributing, but I'm wondering how, since I would need to purge a user in order test this (creation of a new ldap user involves a lot of administrative work) .. and this seems impossible at the moment. Cheers, Matthias P.S. Instance details if of interest: we have a dev instance that uses ldap for authentication, ie users can not create accounts on their own, but the account gets created if they are in ldap. So I have in galaxy.yml `allow_user_creation: false` and in auth_conf ``` Challenge True ``` The configuration worked till recently (LDAP authentication still works according to the logs) -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Helmholtz-Zentrum für Umweltforschung GmbH - UFZ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 1269, Fax +49 341 235 1468 (optional) max.musterm...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Georg Teutsch Administrative Geschäftsführerin/Administrative Managing Director: Dr. Sabine König ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] Re: tool installation problem
Hi Marius, thanks a lot. I solved it. I finally found the reactivate link :) which was unfortunately dysfunctional (https://github.com/galaxyproject/galaxy/issues/7610) .. Best, Matthias On 26.03.19 16:40, Marius van den Beek wrote: Hi Matthias, It might just have been deactivated, in which case you can either activate or uninstall the repo in the admin panel -> Manage tools -> Advanced Search -> Deactivated or Uninstalled. Hope that helps, Marius On Tue, 26 Mar 2019 at 15:59, Matthias Bernt <mailto:m.be...@ufz.de>> wrote: Dear list, I have a problem during installing a tool version that I previously uninstalled. I get the message: `Revision 0696db066a5b of repository deseq2 owned by iuc has already been installed.` It seems to be uninstalled on the file system. Are there any entries that might be left in the DB? Thanks in advance. Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de <mailto:m.be...@ufz.de>, www.ufz.de <http://www.ufz.de> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 1269, Fax +49 341 235 1468 (optional) max.musterm...@ufz.de <mailto:max.musterm...@ufz.de>, www.ufz.de <http://www.ufz.de> Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Georg Teutsch Administrative Geschäftsführerin/Administrative Managing Director: Dr. Sabine König ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Helmholtz-Zentrum für Umweltforschung GmbH - UFZ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 1269, Fax +49 341 235 1468 (optional) max.musterm...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Georg Teutsch Administrative Geschäftsführerin/Administrative Managing Director: Dr. Sabine König ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] Re: tool installation problem
Hi Marius, unfortunately this is not the case, but it's listed as "Uninstalled" when I use the advanced search... Would have been to easy :) Cheers, Matthias On 26.03.19 16:40, Marius van den Beek wrote: Hi Matthias, It might just have been deactivated, in which case you can either activate or uninstall the repo in the admin panel -> Manage tools -> Advanced Search -> Deactivated or Uninstalled. Hope that helps, Marius On Tue, 26 Mar 2019 at 15:59, Matthias Bernt <mailto:m.be...@ufz.de>> wrote: Dear list, I have a problem during installing a tool version that I previously uninstalled. I get the message: `Revision 0696db066a5b of repository deseq2 owned by iuc has already been installed.` It seems to be uninstalled on the file system. Are there any entries that might be left in the DB? Thanks in advance. Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de <mailto:m.be...@ufz.de>, www.ufz.de <http://www.ufz.de> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 1269, Fax +49 341 235 1468 (optional) max.musterm...@ufz.de <mailto:max.musterm...@ufz.de>, www.ufz.de <http://www.ufz.de> Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Georg Teutsch Administrative Geschäftsführerin/Administrative Managing Director: Dr. Sabine König ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Helmholtz-Zentrum für Umweltforschung GmbH - UFZ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 1269, Fax +49 341 235 1468 (optional) max.musterm...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Georg Teutsch Administrative Geschäftsführerin/Administrative Managing Director: Dr. Sabine König ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] tool installation problem
Dear list, I have a problem during installing a tool version that I previously uninstalled. I get the message: `Revision 0696db066a5b of repository deseq2 owned by iuc has already been installed.` It seems to be uninstalled on the file system. Are there any entries that might be left in the DB? Thanks in advance. Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Helmholtz-Zentrum für Umweltforschung GmbH - UFZ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 1269, Fax +49 341 235 1468 (optional) max.musterm...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Georg Teutsch Administrative Geschäftsführerin/Administrative Managing Director: Dr. Sabine König ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] sorry
Dear all, sorry for the last post .. accident. But it actually contained an interesting question: What are currently good approaches for testing workflows? Cheers and sorry again :(, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] Central German Galaxy User Group Meeting 2
Hi Kristian, - Die , oder funktionieren nur für ein einziges Tool? Genau. Wenn man einen ganzen Workflow testen muss, dann kann man das wie machen? Wir hatten dazu mal wft4galaxy benutzt, evtl. gibts noch was besseres? Habe ich selber noch keine Erfahrung mit gemacht. Kannst zum Beispiel mal bei usegalaxy-eu schauen: https://github.com/usegalaxy-eu/workflow-testing/blob/master/.travis.yml https://github.com/usegalaxy-eu/workflow-testing/blob/master/run_galaxy_workflow_tests.sh die scheinen planemo zu nutzen. Waere mal eine passende Frage fuer galaxy-dev@lists.galaxyproject.org ... - Erzeugt PLANEMO sowohl eine Galaxy-XML als auch CONDA-rules? Nein, nur das Galaxy xml. - Wenn ich CONDA Regeln erzeuge, wie gelangt das automatisch nach BIOCONTAINER? Wenn dein recipe in bioconda gemerged wurde wird automatisch ein container mit erzeugt .. soweit ich weiss. - Hast du schon einmal von der Common Tool Description (CTD) gehört? Damit kann man mit einer Tool-Beschreibung Tools für verschiedene Workflow-Systeme erzeugen. Weißt du ob das mittlerweile gut funktioniert? Davon habe ich noch nichts gehoert. Kannst du mir mal einen link schicken - taete mich interessieren. Gruesse, Matthias Viele Grüße, *Kristian On 7. Jan 2019, at 17:46 , Matthias Bernt <mailto:m.be...@ufz.de>> wrote: Hi, wir werden versuchen zumindest den Vormittag per skype zu uebertragen. Am besten einfach mich (mbatle) ab ca 8:45 mal anschreiben. Gruesse, Matthias On 05.01.19 11:50, Peters, Kristian wrote: Hallo Matthias, Januar ist bei mir sehr gefüllt und es sind noch ein paar wichtige Sachen oben drauf gekommen. Daher hatte ich mich vorsichtshalber nicht in den Doodle eingetragen. Vielleicht ist es möglich, per Telefonkonferenz (Hangout, Skype) remote teilzunehmen? Das würde mir viel Zeit am Dienstag ersparen. Viele Grüße, *Kristian On 4. Jan 2019, at 19:40 , Neumann, Steffen <mailto:sneum...@ipb-halle.de> <mailto:sneum...@ipb-halle.de>> wrote: Hi Matthias, ich habe die Koordination von einem grösseren Antrag geerbt, und werde daher am Dienstag nicht nach Leipzig kommen können :-( Kristian hat in den letzten Wochen ebenfalls an einem Workflow für MetFrag gearbeitet, zu dem wir bis jetzt PhenoMeNal packaging haben. Gruss, Steffen On Fri, 2019-01-04 at 18:46 +0100, Matthias Bernt wrote: Dear all, our meeting (workshop on building Galaxy tools and conda packages) will take place next Tuesday (Feb 8th). Below we compiled the most important informations for you. Just write an email if you have any further questions. We are currently expecting the eight participants who registered here: https://dudle.inf.tu-dresden.de/7yxdfay2/. Let me know if you changed you plans. The meeting will take place in the KUBUS (Tagungsbüro 131) at the UFZ. How to reach the UFZ is described here: https://www.ufz.de/index.php?de=34272 The KUBUS is in front of the UFZ. So you don't need to enter through the main gate. Plan: - We will start at 9:00. - For the morning we plan to introduce you to the basics of - building tools for Galaxy with planemo and - building conda packages - For lunch there is a "Kantine" at the UFZ. - In order to practice the learned topics we planned to use the afternoon as a kind of hackaton where you can (start to) build your own Galaxy tool or conda package. We will be there for questions and introduce advanced topics as needed. Therefore it would be great if you 'bring' a tool of your choice, eg your own tool for wrapping, this could be e.g. a shell, R, or python script or some software package that can be compiled. In case that you don't have an idea we have prepared one or two examples. Important: Since some of the required software is quite large we would like to ask you to prepare a few things if possible (at least the first point). 1. You will need a linux command line If your laptop runs Windows you could install VirtualBox and install a linux in this box. Linux images for VirtualBox that are ready to use are available, eg. https://www.osboxes.org/ubuntu/#ubuntu-1804-vbox 2. Download and prepare the bioconda recipes repository - optional: create a fork of https://github.com/bioconda/bioconda-recipes - clone your fork or the main repository, i.e. either `git clone https://github.com/USERNAME/bioconda-recipes` (replace USERNAME) or `git clone https://github.com/bioconda/bioconda-recipes` (see https://bioconda.github.io/contrib-setup.html#git-and-github-one-time-setup ) In the bioconda-recipes root directory call: ``` ./bootstrap.py TEMPORARY_PATH_TO_WHERE_MINICONDA_SHOULD_BE_INSTALLED ``` Replace TEMPORARY_PATH_TO_WHERE_MINICONDA_SHOULD_BE_INSTALLED with some path where miniconda can be installed. (see https://bioconda.github.io/contribute-a-recipe.html#test-locally ) 3. Prepare planemo and Galaxy Install `planemo` via pip or conda as described here: (see https://planemo.readthedocs.io/en/latest/installati
Re: [galaxy-dev] run.sh problem
Hi Dannon, We are trying to run release_18.09. Indeed the output was from planemo, but we get the same (yarn) error when ./run.sh is called without planemo: ``` $ NODE_ENV=production gulp staging && concurrently "yarn run style" "yarn run webpack-production-maps" "yarn run gulp clean && yarn run gulp-production-maps" && yarn run save-build-hash gulp[14831]: ../src/node_contextify.cc:628:static void node::contextify::ContextifyScript::New(const v8::FunctionCallbackInfo&): Assertion `args[1]->IsString()' failed. 1: 0x8daaa0 node::Abort() [gulp] 2: 0x8dab75 [gulp] 3: 0x90e2f7 node::contextify::ContextifyScript::New(v8::FunctionCallbackInfo const&) [gulp] 4: 0xb5e71b [gulp] 5: 0xb606b2 v8::internal::Builtin_HandleApiCall(int, v8::internal::Object**, v8::internal::Isolate*) [gulp] 6: 0x2ce8440dbe1d /tmp/yarn--1546961268610-0.24122682361732672/node: line 3: 14831 Aborted (core dumped) "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/.venv/bin/node" "$@" error Command failed with exit code 134. info Visit https://yarnpkg.com/en/docs/cli/run for documentation about this command. ERROR: Galaxy client build failed. See ./client/README.md for more information, including how to get help. ``` Best, Matthias On 08.01.19 16:09, Dannon Baker wrote: What version of Galaxy exactly is this? And, it looks like it's being run by planemo, and not a simple 'run.sh' via the command line -- is that correct? On Tue, Jan 8, 2019 at 10:04 AM Matthias Bernt <mailto:m.be...@ufz.de>> wrote: Dear all, a colleague tries to run.sh on a Manjaro Linux and got the following error: ``` yarn run v1.12.3 $ NODE_ENV=production gulp staging && concurrently "yarn run style" "yarn run webpack-production-maps" "yarn run gulp clean && yarn run gulp-production-maps" && yarn run save-build-hash gulp[12888]: ../src/node_contextify.cc:628:static void node::contextify::ContextifyScript::New(const v8::FunctionCallbackInfo&): Assertion `args[1]->IsString()' failed. 1: 0x8daaa0 node::Abort() [gulp] 2: 0x8dab75 [gulp] 3: 0x90e2f7 node::contextify::ContextifyScript::New(v8::FunctionCallbackInfo const&) [gulp] 4: 0xb5e71b [gulp] 5: 0xb606b2 v8::internal::Builtin_HandleApiCall(int, v8::internal::Object**, v8::internal::Isolate*) [gulp] 6: 0x6f20bcdbe1d /tmp/yarn--1546955496175-0.8677740791371564/node: line 3: 12888 Aborted (core dumped) "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/.venv/bin/node" "$@" error Command failed with exit code 134. info Visit https://yarnpkg.com/en/docs/cli/run for documentation about this command. ERROR: Galaxy client build failed. See ./client/README.md for more information, including how to get help. Problem running Galaxy command []. Traceback (most recent call last): File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/bin/planemo", line 11, in sys.exit(planemo()) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 764, in __call__ return self.main(*args, **kwargs) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 717, in main rv = self.invoke(ctx) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 1137, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 956, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 555, in invoke return callback(*args, **kwargs) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/decorators.py", line 64, in new_func return ctx.invoke(f, obj, *args, **kwargs) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 555, in invoke return callback(*args, **kwargs) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/cli.py", line 195, in handle_blended_options return f(*args, **kwds) File "/home/henning/nextcloud/PhD
[galaxy-dev] run.sh problem
Dear all, a colleague tries to run.sh on a Manjaro Linux and got the following error: ``` yarn run v1.12.3 $ NODE_ENV=production gulp staging && concurrently "yarn run style" "yarn run webpack-production-maps" "yarn run gulp clean && yarn run gulp-production-maps" && yarn run save-build-hash gulp[12888]: ../src/node_contextify.cc:628:static void node::contextify::ContextifyScript::New(const v8::FunctionCallbackInfo&): Assertion `args[1]->IsString()' failed. 1: 0x8daaa0 node::Abort() [gulp] 2: 0x8dab75 [gulp] 3: 0x90e2f7 node::contextify::ContextifyScript::New(v8::FunctionCallbackInfo const&) [gulp] 4: 0xb5e71b [gulp] 5: 0xb606b2 v8::internal::Builtin_HandleApiCall(int, v8::internal::Object**, v8::internal::Isolate*) [gulp] 6: 0x6f20bcdbe1d /tmp/yarn--1546955496175-0.8677740791371564/node: line 3: 12888 Aborted (core dumped) "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/.venv/bin/node" "$@" error Command failed with exit code 134. info Visit https://yarnpkg.com/en/docs/cli/run for documentation about this command. ERROR: Galaxy client build failed. See ./client/README.md for more information, including how to get help. Problem running Galaxy command []. Traceback (most recent call last): File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/bin/planemo", line 11, in sys.exit(planemo()) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 764, in __call__ return self.main(*args, **kwargs) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 717, in main rv = self.invoke(ctx) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 1137, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 956, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 555, in invoke return callback(*args, **kwargs) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/decorators.py", line 64, in new_func return ctx.invoke(f, obj, *args, **kwargs) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 555, in invoke return callback(*args, **kwargs) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/cli.py", line 195, in handle_blended_options return f(*args, **kwds) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/commands/cmd_serve.py", line 43, in cli galaxy_serve(ctx, runnables, **kwds) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/galaxy/serve.py", line 22, in serve return _serve(ctx, runnables, **kwds) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/galaxy/serve.py", line 54, in _serve raise Exception(message) Exception: Problem running Galaxy command []. ``` Would be great to have a suggestion... Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] tools gone after switching to galaxy.yml
Hi Marius, heureka. That solved it. Thanks a lot. Cheers, Matthias On 19.12.18 13:57, Marius van den Beek wrote: Hi Matthias, if your previous config had a separate database for tools you need to use that. This is controlled by the install_database_connection setting. Best, Marius On Wed, 19 Dec 2018 at 13:53, Matthias Bernt <mailto:m.be...@ufz.de>> wrote: Dear list, just tried to switch to galaxy.yml, which worked in general, but now tools that have been installed from the TS disappeared. In the logs I get for each tool: ``` galaxy.tools.toolbox.base ERROR 2018-12-19 13:28:15,815 [p:22877,w:0,m:0] [MainThread] Error reading tool from path: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/74a8bef53a00/text_processing/cat.xml <http://toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/74a8bef53a00/text_processing/cat.xml> Traceback (most recent call last): File "lib/galaxy/tools/toolbox/base.py", line 563, in _load_tool_tag_set tool_shed_repository = self.get_tool_repository_from_xml_item(item, path) File "lib/galaxy/tools/toolbox/base.py", line 629, in get_tool_repository_from_xml_item raise Exception(msg) Exception: Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database ``` Any idea what could be wrong here? The connection to the DB seems to be functional, since I can see the users in the admin Panel. Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de <mailto:m.be...@ufz.de>, www.ufz.de <http://www.ufz.de> Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] tools gone after switching to galaxy.yml
Dear list, just tried to switch to galaxy.yml, which worked in general, but now tools that have been installed from the TS disappeared. In the logs I get for each tool: ``` galaxy.tools.toolbox.base ERROR 2018-12-19 13:28:15,815 [p:22877,w:0,m:0] [MainThread] Error reading tool from path: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/74a8bef53a00/text_processing/cat.xml Traceback (most recent call last): File "lib/galaxy/tools/toolbox/base.py", line 563, in _load_tool_tag_set tool_shed_repository = self.get_tool_repository_from_xml_item(item, path) File "lib/galaxy/tools/toolbox/base.py", line 629, in get_tool_repository_from_xml_item raise Exception(msg) Exception: Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database ``` Any idea what could be wrong here? The connection to the DB seems to be functional, since I can see the users in the admin Panel. Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] number of elements in collections and multiple-true-params
Hi Marius, I think you're right in that len($input_type.input_bam) is inconsistent, we can implement __len__ for the collection case, but that is not done yet. ThumbsUp! Would be for the tool developer convenience. That said, unless your example is a toy example for a more complex scenario the switch seems unnecessary, a multiple="true" data paramater can take either multiple datasets or a collection. You are right, still you could replace the list with a paired list or list list. Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] number of elements in collections and multiple-true-params
Dear list, in a tool I want to process a set of (bam) files. For the convenience of the user I thought that it would be nice to allow collections as well as manually selected files (in a param with multiple=true). Like so: ``` data set list data sets multiple="true" optional="false" label="BAM files" /> collection_type="list" label="BAM files" /> ``` Is there a way to get the number of data sets in both cases (in the collection or selection) in a consistent way? Currently the only way I found is: ``` #if $input_type.input_type_selector == 'manual': #set count = len($input_type.input_bam) #else #set count = len($input_type.input_bam.keys()) #end if ``` Appart from this looping works like a charm: ``` #for $bam in $input_type.input_bam: OPERATIONS... #end for ``` Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] Search box in tools menu / uncomplete wrappers list
Hi, I observed similar Problems on my Galaxy. But I think not all cases can be explained by Martins answer. For instance, if I search for "hisat" I don't get any result, but HISAT2 is definitely installed. Cheers, Matthias Message: 1 Date: Fri, 9 Nov 2018 15:54:16 + From: Sarah Maman To: "galaxy-dev@lists.galaxyproject.org" Subject: [galaxy-dev] Search box in tools menu / uncomplete wrappers list Message-ID: <1541778855881.43...@inra.fr> Content-Type: text/plain; charset="iso-8859-1" Hello, When I'm searching a keyword in the « search » box in left « tools » menu, results are sometimes false because the wrappers' list generated by the query thanks to a keyword is not full, some tools are missing. In fact, some wrappers are not listed even if the keyword is in the tool name and/or the tool description. Could you please help us to understand why ? Thanks, Sarah Maman _ Sarah Maman Bioinformatique/Bioinformatics INRA | SIGENAE | GenPhySE Centre Inra Occitanie-Toulouse Tél. : +33(0)5.61.28.57.08 _ Chemin de Borde Rouge CS 52627 31326 Castanet Tolosan cedex www.toulouse.inra.fr<http://www.toulouse.inra.fr/> Suivez-nous sur Twitter ! -- next part -- An HTML attachment was scrubbed... URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20181109/5edcc351/attachment-0001.html> -- Message: 2 Date: Fri, 9 Nov 2018 12:13:53 -0500 From: Martin Čech To: Sarah Maman Cc: "galaxy-dev@lists.galaxyproject.org" Subject: Re: [galaxy-dev] Search box in tools menu / uncomplete wrappers list Message-ID: Content-Type: text/plain; charset="utf-8" Hi Sarah, toolpanel search in Galaxy is configurable. Due to limited space the default number of results shown is 20 so if there are more you are not going to see them. You can also change weights of various search attributes or use ngram search. Please see the config options explained in the sample here: https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.yml.sample#L1147 Please, let us know if you have more questions. Thanks, Martin On Fri, Nov 9, 2018 at 12:04 PM Sarah Maman wrote: Hello, When I’m searching a keyword in the « search » box in left « tools » menu, results are sometimes false because the wrappers' list generated by the query thanks to a keyword is not full, some tools are missing. In fact, some wrappers are not listed even if the keyword is in the tool name and/or the tool description. Could you please help us to understand why ? Thanks, Sarah Maman *_ **Sarah* *Maman* Bioinformatique/Bioinformatics INRA | SIGENAE | GenPhySE *Centre Inra Occitanie-Toulouse *Tél. : +33(0)5.61.28.57.08 <+33%205%2061%2028%2057%2008> *_* Chemin de Borde Rouge CS 52627 31326 Castanet Tolosan cedex *www.toulouse.inra.fr* <http://www.toulouse.inra.fr/> *Suivez-nous sur Twitter !* ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ -- next part -- An HTML attachment was scrubbed... URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20181109/0c7c7b43/attachment-0001.html> -- Subject: Digest Footer ___ galaxy-dev mailing list galaxy-dev@lists.galaxyproject.org https://lists.galaxyproject.org/listinfo/galaxy-dev To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- End of galaxy-dev Digest, Vol 149, Issue 3 ****** -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch --- ___ Please keep all replies on the list by using "reply all" in your mail
Re: [galaxy-dev] tool data confusion
Hi Peter, then the I need to update all the paths in: `config/shed_tool_data_table_conf.xml`? Because currently the $GALAXY/tool-data/*.loc files are ignored in my instance. For me it looks like a bug (caused by a misconfiguration?) that there are all xml files refer to the same loc file. Wouldn't this be more useful: - config/shed_tool_data_table_conf.xml -> tool-data/diamond_database.loc - tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/tool_data_table_conf.xml -> tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/diamond_database.loc Best, Matthias On 02.10.2018 11:22, Peter Cock wrote: Personally I tend to work with $GALAXY/tool-data/*.loc (and ignore the tool shed installed copies in their cryptically named folders) but this reflects in part the fact that this used to be the only copy of the file, and that's just what I always did. If you use a data manager, I don't know which copy it updates - but the merging design is meant to hide these details I suppose. Peter On Mon, Oct 1, 2018 at 5:56 PM Matthias Bernt wrote: Dear list, I still have problems to get my head around tool data. Lets consider diamond for example (lets ignore data managers for the moment). After installation it seems that there are two relevant xml files: - `config/shed_tool_data_table_conf.xml` - `tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/tool_data_table_conf.xml` and two loc files: - `tool-data/diamond_database.loc` - `tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/diamond_database.loc` In both xml files the latter loc file is referenced. And therefor the tool-data/diamond_database.loc file is seemingly ignored. What is the rational to have a loc and xml file for each tool version? It seems that they are merged upon startup anyway. What would be the best way to administrate a single tool loc file? Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] tool data confusion
Dear list, I still have problems to get my head around tool data. Lets consider diamond for example (lets ignore data managers for the moment). After installation it seems that there are two relevant xml files: - `config/shed_tool_data_table_conf.xml` - `tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/tool_data_table_conf.xml` and two loc files: - `tool-data/diamond_database.loc` - `tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/diamond_database.loc` In both xml files the latter loc file is referenced. And therefor the tool-data/diamond_database.loc file is seemingly ignored. What is the rational to have a loc and xml file for each tool version? It seems that they are merged upon startup anyway. What would be the best way to administrate a single tool loc file? Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] java options
Hi Bjoern, So, it seems that the best option is to: - switching back to _JAVA_OPTIONS (which seems to be implemented also on usegalaxy.org) - handling the output in each java tool This is also what usegalaxy.eu is using and we have special destinations for java tools. Indeed, this seems to be the best option. Are there any guidelines for wrapping java based applications (or other programming languages)? - add java to dependencies? I think this should be done, or? This should be part of the dependencies of your tool already, isn't it? So MSGFplus should depend on a java version of their choice. See here: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/msgf_plus/meta.yaml#L15 I still tend to forget that conda also has dependencies .. of course this makes more sense than having a galaxy dependency. - if yes: is there a favored conda package? openjdk if needed. OK. Thanks also to you. Best, Matthias Ciao, Bjoern Cheers, Matthias P.S. I just added java to my list of despicable programming languages. On 27.08.2018 12:00, Marius van den Beek wrote: Hi Matthias, if a tool prints something to the stderr that is indeed considered to indicate a failure, and it's the default mostly because we don't want to break legacy tools that make this assumption. If you include a profile version in your tool or change your command section to detect_errors="exit_code"> this will more reasonably determine if a tool failed based on the exit code. Best, Marius On Mon, 27 Aug 2018 at 11:52, Matthias Bernt <mailto:m.be...@ufz.de>> wrote: Dear list, I'm struggling to set java options for galaxy tools. Currently I use ` in my job_conf.xml and in the script I explored two ways to set java options: `_JAVA_OPTIONS="-Xmx5G -Xms1G -Djava.io.tmpdir=/work/songalax/tmp"` But then java prints "Picked up _JAVA_OPTIONS: ..." to stderr which is be interpreted as error by some tools. If I'm correct this is currently the default .. I have seen this happening, but can't remember the name of the tool. So I switched to this 'trick': `alias java='java -Xmx5G -Xms1G -Djava.io.tmpdir=/work/songalax/tmp'` but the problem is that the tool script is called and not sourced and therefore aliases are not used (could this be changed?). Furthermore, for tools which explicitly set the java options my settings would be ignored anyway (an example is the MSGFPlusAdapter which calles `java -Xmx3500m` .. so my -Xmx is overwritten .. I passing GALAXY_MEMORY_MB to the corresponding parameter might be a solution for this tool). Any thought or suggestions on how to set the parameters in a production environment are very welcome. Cheers, Matthias -- ------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de <mailto:m.be...@ufz.de>, www.ufz.de <http://www.ufz.de> Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___
Re: [galaxy-dev] java options
Hi Marius, Thanks for your comments. That's what I thought. > To me this sounds like something that really should be fixed in the > tool as presumably this affects every deployer. Hmm. The 'tool' would be java. As far as I have seen java is never/seldom in the tool dependencies. Hence, the system's java installation is used for which we do not know if it is Sun/OpenJDK or which version it is (in addition the installation will likely not change on production systems for a long time). So I guess fixing this in java would not help here in reasonable time anyway. So, it seems that the best option is to: - switching back to _JAVA_OPTIONS (which seems to be implemented also on usegalaxy.org) - handling the output in each java tool Are there any guidelines for wrapping java based applications (or other programming languages)? - add java to dependencies? I think this should be done, or? - if yes: is there a favored conda package? Cheers, Matthias P.S. I just added java to my list of despicable programming languages. On 27.08.2018 12:00, Marius van den Beek wrote: Hi Matthias, if a tool prints something to the stderr that is indeed considered to indicate a failure, and it's the default mostly because we don't want to break legacy tools that make this assumption. If you include a profile version in your tool or change your command section to detect_errors="exit_code"> this will more reasonably determine if a tool failed based on the exit code. Best, Marius On Mon, 27 Aug 2018 at 11:52, Matthias Bernt <mailto:m.be...@ufz.de>> wrote: Dear list, I'm struggling to set java options for galaxy tools. Currently I use ` in my job_conf.xml and in the script I explored two ways to set java options: `_JAVA_OPTIONS="-Xmx5G -Xms1G -Djava.io.tmpdir=/work/songalax/tmp"` But then java prints "Picked up _JAVA_OPTIONS: ..." to stderr which is be interpreted as error by some tools. If I'm correct this is currently the default .. I have seen this happening, but can't remember the name of the tool. So I switched to this 'trick': `alias java='java -Xmx5G -Xms1G -Djava.io.tmpdir=/work/songalax/tmp'` but the problem is that the tool script is called and not sourced and therefore aliases are not used (could this be changed?). Furthermore, for tools which explicitly set the java options my settings would be ignored anyway (an example is the MSGFPlusAdapter which calles `java -Xmx3500m` .. so my -Xmx is overwritten .. I passing GALAXY_MEMORY_MB to the corresponding parameter might be a solution for this tool). Any thought or suggestions on how to set the parameters in a production environment are very welcome. Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de <mailto:m.be...@ufz.de>, www.ufz.de <http://www.ufz.de> Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- _
[galaxy-dev] java options
Dear list, I'm struggling to set java options for galaxy tools. Currently I use ` in my job_conf.xml and in the script I explored two ways to set java options: `_JAVA_OPTIONS="-Xmx5G -Xms1G -Djava.io.tmpdir=/work/songalax/tmp"` But then java prints "Picked up _JAVA_OPTIONS: ..." to stderr which is be interpreted as error by some tools. If I'm correct this is currently the default .. I have seen this happening, but can't remember the name of the tool. So I switched to this 'trick': `alias java='java -Xmx5G -Xms1G -Djava.io.tmpdir=/work/songalax/tmp'` but the problem is that the tool script is called and not sourced and therefore aliases are not used (could this be changed?). Furthermore, for tools which explicitly set the java options my settings would be ignored anyway (an example is the MSGFPlusAdapter which calles `java -Xmx3500m` .. so my -Xmx is overwritten .. I passing GALAXY_MEMORY_MB to the corresponding parameter might be a solution for this tool). Any thought or suggestions on how to set the parameters in a production environment are very welcome. Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] tool datatypes
Hi, thanks for your support. This helps. I have thought a bit about composite data types. And have additional questions. In my case the additional data is essentially a folder (w subfolders). The contents of the folder vary (it depends on the input of the programs that generate them). So the question is if I can/should - add a single folder (with all the hirarchy as a single composite data element) .. I have only seen a add_composite_file function. - add a dynamic number of composite files - or if it is better to use the extra_files_path mechanism (which seems to be the simplest for me) In any of these cases my next question would be how to create a test using such a data as input and output (for output I have seen an example somewhere). Cheers, Matthias On 17.08.2018 11:53, Peter Cock wrote: This is probably a John Chilton question, as the Planemo lead. The way I do it is to "manually" install the datatype into a Galaxy test instance (adding entries to the datatypes_conf.xml and Python files to Galaxy's internal library), and then call ``planemo test`` pointing at this test instance. You can see that approach in action here: https://github.com/peterjc/galaxy_blast/blob/579c348ced72d4e6f1ef7fb0cded98e52f454b92/.travis.yml#L106 https://github.com/peterjc/galaxy_blast/blob/579c348ced72d4e6f1ef7fb0cded98e52f454b92/.travis.datatypes_conf.xml#L20 and: https://github.com/peterjc/galaxy_mira/blob/206259620376b322fc8ed99a6efdd3712f38764b/.travis.yml#L113 https://github.com/peterjc/galaxy_mira/blob/206259620376b322fc8ed99a6efdd3712f38764b/.travis.datatypes_conf.xml#L42 There may be a more elegant solution nowadays using planemo to do some of the work. Peter On Thu, Aug 16, 2018 at 9:30 PM, Matthias Bernt wrote: Dear Peter, you are right. I hope that this will be much less in the end (I'm still learning about the package). The main question still remains, how do I get `planemo test` to include the data types defined in the xml file? Best, Matthias Am 16/08/18 18:32 schrieb Peter Cock : Defining 20 different text-based formats does not look ideal (if that is what you are doing). Do you have sample output in the repository? Perhaps at least some of these can be better defined as tabular instead? Or, perhaps you can define one composite datatype for the folder of output instead? Peter On Thu, Aug 16, 2018 at 4:18 PM, Matthias Bernt wrote: Hi Peter, I hope that subclassing simple data types will be sufficient. More details: I'm currently trying to (auto)wrap the checkm suite https://github.com/Ecogenomics/CheckM. Current state here: https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/checkm. These tools often create an output folder which is then the input to other tools. So I thought to create a (output) data type for each of the tools and save the folder using extra_files_path. Then I can pass the folder to downstream tools (and can check for proper input). I hope that subclassing txt or tabular will be sufficient. Cheers, Matthias On 16.08.2018 17:02, Peter Cock wrote: More details might help - are you just defining the new datatype as a subclass in the XML, or do you need to include Python code (e.g. for a sniffer)? If you want to see some examples of datatypes using Python code which are available via the Tool Shed, here are two: https://github.com/peterjc/galaxy_blast/tree/master/data_managers/ncbi_blastdb (now also in the Galaxy core) https://github.com/peterjc/galaxy_mira/tree/master/datatypes/mira_datatypes Peter On Thu, Aug 16, 2018 at 3:48 PM, Matthias Bernt wrote: Dear list, just a request for links to documentation: How can I realize tool specific data types. I'm just developing a set of tools that need their own data types, but I don't want to add them to Galaxy's core data types (yet). I've seen examples of tools that had a datatypes_conf.xml. So I created one, but it seems that it is ignored. Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, plea
Re: [galaxy-dev] tool datatypes
Dear Peter, you are right. I hope that this will be much less in the end (I'm still learning about the package). The main question still remains, how do I get `planemo test` to include the data types defined in the xml file? Best, Matthias Am 16/08/18 18:32 schrieb Peter Cock : > > Defining 20 different text-based formats does not look ideal (if that > is what you are doing). > > Do you have sample output in the repository? Perhaps at least some of > these can be better defined as tabular instead? > > Or, perhaps you can define one composite datatype for the folder of > output instead? > > Peter > > On Thu, Aug 16, 2018 at 4:18 PM, Matthias Bernt wrote: > > Hi Peter, > > > > I hope that subclassing simple data types will be sufficient. > > > > More details: > > > > I'm currently trying to (auto)wrap the checkm suite > > https://github.com/Ecogenomics/CheckM. Current state here: > > https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/checkm. > > > > These tools often create an output folder which is then the input to other > > tools. So I thought to create a (output) data type for each of the tools and > > save the folder using extra_files_path. Then I can pass the folder to > > downstream tools (and can check for proper input). I hope that subclassing > > txt or tabular will be sufficient. > > > > Cheers, > > Matthias > > > > > > > > On 16.08.2018 17:02, Peter Cock wrote: > >> > >> More details might help - are you just defining the new datatype as a > >> subclass in the XML, or do you need to include Python code (e.g. for a > >> sniffer)? > >> > >> If you want to see some examples of datatypes using Python code which > >> are available via the Tool Shed, here are two: > >> > >> > >> https://github.com/peterjc/galaxy_blast/tree/master/data_managers/ncbi_blastdb > >> (now also in the Galaxy core) > >> > >> https://github.com/peterjc/galaxy_mira/tree/master/datatypes/mira_datatypes > >> > >> Peter > >> > >> On Thu, Aug 16, 2018 at 3:48 PM, Matthias Bernt wrote: > >>> > >>> Dear list, > >>> > >>> just a request for links to documentation: How can I realize tool > >>> specific > >>> data types. I'm just developing a set of tools that need their own data > >>> types, but I don't want to add them to Galaxy's core data types (yet). > >>> > >>> I've seen examples of tools that had a datatypes_conf.xml. So I created > >>> one, > >>> but it seems that it is ignored. > >>> > >>> Cheers, > >>> Matthias > >>> > >>> > >>> -- > >>> > >>> --- > >>> Matthias Bernt > >>> Bioinformatics Service > >>> Molekulare Systembiologie (MOLSYB) > >>> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ > >>> Helmholtz Centre for Environmental Research GmbH - UFZ > >>> Permoserstraße 15, 04318 Leipzig, Germany > >>> Phone +49 341 235 482296, > >>> m.be...@ufz.de, www.ufz.de > >>> > >>> Sitz der Gesellschaft/Registered Office: Leipzig > >>> Registergericht/Registration Office: Amtsgericht Leipzig > >>> Handelsregister Nr./Trade Register Nr.: B 4703 > >>> Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: > >>> MinDirig > >>> Wilfried Kraus > >>> Wissenschaftlicher Geschäftsführer/Scientific Managing Director: > >>> Prof. Dr. Dr. h.c. Georg Teutsch > >>> Administrative Geschäftsführerin/ Administrative Managing Director: > >>> Prof. Dr. Heike Graßmann > >>> --- > >>> ___ > >>> Please keep all replies on the list by using "reply all" > >>> in your mail client. To manage your subscriptions to this > >>> and other Galaxy lists, please use the interface at: > >>> https://lists.galaxyproject.org/ > >>> > >>> To search Galaxy mailing lists use the unified search at: > >>> http://galaxyproject.org/search/ > > > > > > -- > > > > --- > > Matthias Bernt > > Bioinformatics Service > > Molekulare Systembiologie (MOLSYB) > > Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ > > Helm
Re: [galaxy-dev] tool datatypes
Hi Peter, I hope that subclassing simple data types will be sufficient. More details: I'm currently trying to (auto)wrap the checkm suite https://github.com/Ecogenomics/CheckM. Current state here: https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/checkm. These tools often create an output folder which is then the input to other tools. So I thought to create a (output) data type for each of the tools and save the folder using extra_files_path. Then I can pass the folder to downstream tools (and can check for proper input). I hope that subclassing txt or tabular will be sufficient. Cheers, Matthias On 16.08.2018 17:02, Peter Cock wrote: More details might help - are you just defining the new datatype as a subclass in the XML, or do you need to include Python code (e.g. for a sniffer)? If you want to see some examples of datatypes using Python code which are available via the Tool Shed, here are two: https://github.com/peterjc/galaxy_blast/tree/master/data_managers/ncbi_blastdb (now also in the Galaxy core) https://github.com/peterjc/galaxy_mira/tree/master/datatypes/mira_datatypes Peter On Thu, Aug 16, 2018 at 3:48 PM, Matthias Bernt wrote: Dear list, just a request for links to documentation: How can I realize tool specific data types. I'm just developing a set of tools that need their own data types, but I don't want to add them to Galaxy's core data types (yet). I've seen examples of tools that had a datatypes_conf.xml. So I created one, but it seems that it is ignored. Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] tool datatypes
Dear list, just a request for links to documentation: How can I realize tool specific data types. I'm just developing a set of tools that need their own data types, but I don't want to add them to Galaxy's core data types (yet). I've seen examples of tools that had a datatypes_conf.xml. So I created one, but it seems that it is ignored. Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] Conda problems: Failed to activate conda environment
Hi Gerhard,
wonderful.
For the other problem: you seem to use a tool that still uses a toolshed
package (python in this case) instead of the conda dependency. Can you
make sure that you ensure that conda is used for dependency resolution?
Otherwise, which tool are you trying to install?
Cheers,
Matthias
On 06.07.2018 10:38, Van Wageningen, GERHARD [gerha...@sun.ac.za] wrote:
Hi Matthias - thanx for the missing link tip - that fixes that ...
Locale as Galaxy user is
[galaxy@storage1 ~]$ locale
LANG=en_US.UTF-8
LC_CTYPE="en_US.UTF-8"
LC_NUMERIC="en_US.UTF-8"
LC_TIME="en_US.UTF-8"
LC_COLLATE="en_US.UTF-8"
LC_MONETARY="en_US.UTF-8"
LC_MESSAGES="en_US.UTF-8"
LC_PAPER="en_US.UTF-8"
LC_NAME="en_US.UTF-8"
LC_ADDRESS="en_US.UTF-8"
LC_TELEPHONE="en_US.UTF-8"
LC_MEASUREMENT="en_US.UTF-8"
LC_IDENTIFICATION="en_US.UTF-8"
LC_ALL=
*From:* Matthias Bernt
*Sent:* 06 July 2018 10:15:12
*To:* Van Wageningen, GERHARD [gerha...@sun.ac.za]
*Cc:* galaxy-dev@lists.galaxyproject.org
*Subject:* Re: Conda problems: Failed to activate conda environment
Dear Gerhard,
I don't know about the python error.. could you tell us the output of
`locale` when logged in as the user running the Galaxy server?
For the second problem, I remember that I also have a similar problem.
For some reasons some symlinks in the conda environment are not created.
you can check if in the respective environment's bin directory symlinks
to the conda, activate and deactivate binaries/scripts exist.
If not you can fix the missing links (I run the following after each
tool installation)
```
for env in "{{ galaxy_server_dir }}"/database/dependencies/_conda/envs/*; do
for link in conda activate deactivate; do
\[ -h $env/bin/$link \] || ln -s "{{ galaxy_server_dir
}}"/database/dependencies/_conda/bin/$link $env/bin/$link;
done
done
```
Hope this helps.
Cheers,
Matthias
On 05.07.2018 18:00, galaxy-dev-requ...@lists.galaxyproject.org wrote:
Message: 1
Date: Thu, 5 Jul 2018 08:14:35 +
From: "Van Wageningen, GERHARD [gerha...@sun.ac.za]"
To:"galaxy-dev@lists.galaxyproject.org"
Subject: [galaxy-dev] Conda problems: Failed to activate conda
environment
Message-ID:
Content-Type: text/plain; charset="iso-8859-1"
Hi All
I have recently started learning the Galaxy setup starting with an upgrade.
Made some headway but I was wondering if someone could comment on a problem
that has emerged.
The system is a Galaxy 18.05 installation (upgraded from 17.01) on an Altair
PBS scheduler with drmaa setup (working)
Conda problem: Failed to activate conda environment.
Conda works during tool installation or reinstallation.
Galaxy tools have been updated/reinstalled so they all look "green" in manage
tools.
In Manage Dependencies there are a number of "Dependency resolved but version not
found" warnings, otherwise the deps look clean.
When running tools in Galaxy errors occur, after the jobs have correctly
deployed on the cluster.
The galaxy application raised errors like the two below.
"Failed to activate conda environment! Error was:
Fatal Python error: Py_Initialize: Unable to get the locale encoding
File
"/home/.galaxy/tooldeps/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/__init__.py",
line 123
raise C"
"
Failed to activate conda environment! Error was: CondaEnvironmentError:
Environment error: Cannot activate environment bash. User does not have write
access for conda symlinks.
"
Galaxy started and stopped using supervisord with config below:
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
<http://www.sun.ac.za/english/Pages/Water-crisis.aspx>
The integrity and confidentiality of this email is governed by these
terms. Disclaimer <http://www.sun.ac.za/emaildisclaimer >
Die integriteit en vertroulikheid van hierdie e-pos word deur die
volgende bepalings gereël. Vrywaringsklousul
Re: [galaxy-dev] Conda problems: Failed to activate conda environment
Dear Gerhard,
I don't know about the python error.. could you tell us the output of
`locale` when logged in as the user running the Galaxy server?
For the second problem, I remember that I also have a similar problem.
For some reasons some symlinks in the conda environment are not created.
you can check if in the respective environment's bin directory symlinks
to the conda, activate and deactivate binaries/scripts exist.
If not you can fix the missing links (I run the following after each
tool installation)
```
for env in "{{ galaxy_server_dir }}"/database/dependencies/_conda/envs/*; do
for link in conda activate deactivate; do
\[ -h $env/bin/$link \] || ln -s "{{ galaxy_server_dir
}}"/database/dependencies/_conda/bin/$link $env/bin/$link;
done
done
```
Hope this helps.
Cheers,
Matthias
On 05.07.2018 18:00, galaxy-dev-requ...@lists.galaxyproject.org wrote:
Message: 1
Date: Thu, 5 Jul 2018 08:14:35 +
From: "Van Wageningen, GERHARD [gerha...@sun.ac.za]"
To:"galaxy-dev@lists.galaxyproject.org"
Subject: [galaxy-dev] Conda problems: Failed to activate conda
environment
Message-ID:
Content-Type: text/plain; charset="iso-8859-1"
Hi All
I have recently started learning the Galaxy setup starting with an upgrade.
Made some headway but I was wondering if someone could comment on a problem
that has emerged.
The system is a Galaxy 18.05 installation (upgraded from 17.01) on an Altair
PBS scheduler with drmaa setup (working)
Conda problem: Failed to activate conda environment.
Conda works during tool installation or reinstallation.
Galaxy tools have been updated/reinstalled so they all look "green" in manage
tools.
In Manage Dependencies there are a number of "Dependency resolved but version not
found" warnings, otherwise the deps look clean.
When running tools in Galaxy errors occur, after the jobs have correctly
deployed on the cluster.
The galaxy application raised errors like the two below.
"Failed to activate conda environment! Error was:
Fatal Python error: Py_Initialize: Unable to get the locale encoding
File
"/home/.galaxy/tooldeps/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/__init__.py",
line 123
raise C"
"
Failed to activate conda environment! Error was: CondaEnvironmentError:
Environment error: Cannot activate environment bash. User does not have write
access for conda symlinks.
"
Galaxy started and stopped using supervisord with config below:
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/
[galaxy-dev] jobs not running with galaxy.yml
Dear list, I'm trying to switch from galaxy.ini to yml on my dev instance (using a drmaa runner starting jobs as real user). Somehow my jobs are not starting anymore (it seems that they are not given to the job handler). The only output I get is: galaxy.tools.actions INFO 2018-06-27 13:11:37,445 [p:19863,w:1,m:0] [uWSGIWorker1Core2] Handled output named output for tool idba_ud (25965.752 ms) galaxy.tools.actions INFO 2018-06-27 13:11:37,459 [p:19863,w:1,m:0] [uWSGIWorker1Core2] Added output datasets to history (13.657 ms) galaxy.tools.actions INFO 2018-06-27 13:11:37,484 [p:19863,w:1,m:0] [uWSGIWorker1Core2] Verified access to datasets for Job[unflushed,tool_id=idba_ud] (5.423 ms) galaxy.tools.actions INFO 2018-06-27 13:11:37,484 [p:19863,w:1,m:0] [uWSGIWorker1Core2] Setup for job Job[unflushed,tool_id=idba_ud] complete, ready to flush (25.058 ms) galaxy.tools.actions INFO 2018-06-27 13:11:37,522 [p:19863,w:1,m:0] [uWSGIWorker1Core2] Flushed transaction for job Job[id=4366,tool_id=idba_ud] (37.777 ms) galaxy.tools.execute DEBUG 2018-06-27 13:11:37,522 [p:19863,w:1,m:0] [uWSGIWorker1Core2] Tool [idba_ud] created job [4366] (26050.612 ms) galaxy.tools.execute DEBUG 2018-06-27 13:11:37,538 [p:19863,w:1,m:0] [uWSGIWorker1Core2] Executed 1 job(s) for tool idba_ud request: (26075.593 ms) In addition to manual conversion I tried the auto conversion using `make config-convert` with the same result. I also tried to validate the yml file: ``` make config-validate ``` but get only: ``` pykwalify.errors.RuleError: match: 'None' --> '': Path: '/mapping/galaxy/mapping/error_email_to'> ``` Any ideas where I could start digging? Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] instance management inspiration
Hi Bjoern, nothing really fancy for usegalaxy.eu but we maintain this repo here: https://github.com/usegalaxy-eu/usegalaxy-eu-tools We have agreed on a set of labels and lint the tools against this white list. The tools are installed automatically with ephemeris. Cool. Is there also a mechanism for ordering the toolpanel? Or do you do this manually? If so, how? Via the integrated toolpanel xml file? Quotas are managed manually to a large degree, as we do not have that many different once. OK. Thanks a lot for your reply. Cheers, Bjoern Am 20.06.2018 um 15:54 schrieb Matthias Bernt: Dear list, I'm looking for some inspiration for managing my galaxy instance (with ansible). In particular I'm looking for ansible roles to - setup quotas - manage the tool panel (I need to get order in the chaos) I'm wondering how the usegalaxy instances manage this? Is there some github that I could browse? Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] instance management inspiration
Dear list, I'm looking for some inspiration for managing my galaxy instance (with ansible). In particular I'm looking for ansible roles to - setup quotas - manage the tool panel (I need to get order in the chaos) I'm wondering how the usegalaxy instances manage this? Is there some github that I could browse? Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] job deletion
Dear list, i stumbled over a little problem in the implementation of my univa/drmaa job runner (https://github.com/galaxyproject/galaxy/pull/4857) which gets its information from qacct. The problem is that jobs that are deleted before they start are not stored in the job accounting data base which is used by qacct. Is there a way to determine that a job was deleted from the Galaxy job properties? It seems that in the stop_job method of the drmaa runner does not record anywhere that the job was deleted... Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] galaxy upgrade 18.05 problem
Dear list, after upgrading to 18.05 I get an empty page when opening the galaxy website. The proxy logs say: [Mon Jun 11 15:20:10 2018] [error] [client 141.65.5.81] File does not exist: /data/galaxy_server/galaxy/static/scripts/packed, referer: https://galaxy.intranet.ufz.de/root/login?redirect=%2F Which is true, ie. the file/directory does not exist. Any ideas which step I forgot during the upgrade? Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] tabular data display
Dear Dannon, I will talk to our users first and see if filtering columns is applicable for this 'monster'. IMHO 50 columns are not nice to look at anyway, but some sort of filtering or aggregate statistics should be applied anyway. Cheers, Matthias On 01.06.2018 16:14, Dannon Baker wrote: Yeah, it was intentional to avoid browser crashes years ago with very large tables. 50 was somewhat arbitrarily chosen, at the time. We could make this configurable for galaxy instances and/or increase it outright. Here's the logic in question, if you wanted to tinker with it: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/tabular.py#L90 On Fri, Jun 1, 2018 at 10:04 AM Matthias Bernt <mailto:m.be...@ufz.de>> wrote: Dear Dannon, its 59 columns :( the last columns are only sometimes 0. Is there a performance issue when rendering html tables with a larger number of columns? What would be the Galaxy way to handle data with a larger number of columns? I agree that the scidx problem is unrelated. Might be worth to open an issue? Best, Matthias On 01.06.2018 15:44, Dannon Baker wrote: > I'm not familiar with MetaProSIP, but how many columns *should* be in > the output? Galaxy automatically displays tabular data with more than > 50 columns in the 'raw' view you're seeing here, instead of using a > table. The last bit of data in particular, when looking at the sample, > is a ton of `0` columns. Is that correct? > > One more possible issue is that this is sniffed as a `scidx` file, for > me, though that's unrelated to the display problem here. > > -Dannon > > On Fri, Jun 1, 2018 at 9:03 AM Matthias Bernt mailto:m.be...@ufz.de> > <mailto:m.be...@ufz.de <mailto:m.be...@ufz.de>>> wrote: > > Dear list, > > I'm struggling with tabular data in Galaxy. Attached is a tab separated > file that is generated by MetaProSIP (an updated - not yet committed -- > version). > > The problem is that it is not shown as table in Galaxy (dev) at all. > Also the peek preview is odd, some values of the header and data are > omitted. > > Is this a bug in Galaxy, or of the data in the table? > > Cheers, > Matthias > -- > > --- > Matthias Bernt > Bioinformatics Service > Molekulare Systembiologie (MOLSYB) > Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ > Helmholtz Centre for Environmental Research GmbH - UFZ > Permoserstraße 15, 04318 Leipzig, Germany > Phone +49 341 235 482296, > m.be...@ufz.de <mailto:m.be...@ufz.de> <mailto:m.be...@ufz.de <mailto:m.be...@ufz.de>>, www.ufz.de <http://www.ufz.de> <http://www.ufz.de> > > Sitz der Gesellschaft/Registered Office: Leipzig > Registergericht/Registration Office: Amtsgericht Leipzig > Handelsregister Nr./Trade Register Nr.: B 4703 > Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: > MinDirig Wilfried Kraus > Wissenschaftlicher Geschäftsführer/Scientific Managing Director: > Prof. Dr. Dr. h.c. Georg Teutsch > Administrative Geschäftsführerin/ Administrative Managing Director: > Prof. Dr. Heike Graßmann > --- > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ > -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de <mailto:m.be...@ufz.de>, www.ufz.de <http://www.ufz.de> Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Direc
Re: [galaxy-dev] tabular data display
Dear Dannon,
its 59 columns :( the last columns are only sometimes 0.
Is there a performance issue when rendering html tables with a larger
number of columns?
What would be the Galaxy way to handle data with a larger number of
columns?
I agree that the scidx problem is unrelated. Might be worth to open an
issue?
Best,
Matthias
On 01.06.2018 15:44, Dannon Baker wrote:
I'm not familiar with MetaProSIP, but how many columns *should* be in
the output? Galaxy automatically displays tabular data with more than
50 columns in the 'raw' view you're seeing here, instead of using a
table. The last bit of data in particular, when looking at the sample,
is a ton of `0` columns. Is that correct?
One more possible issue is that this is sniffed as a `scidx` file, for
me, though that's unrelated to the display problem here.
-Dannon
On Fri, Jun 1, 2018 at 9:03 AM Matthias Bernt <mailto:m.be...@ufz.de>> wrote:
Dear list,
I'm struggling with tabular data in Galaxy. Attached is a tab separated
file that is generated by MetaProSIP (an updated - not yet committed --
version).
The problem is that it is not shown as table in Galaxy (dev) at all.
Also the peek preview is odd, some values of the header and data are
omitted.
Is this a bug in Galaxy, or of the data in the table?
Cheers,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de <mailto:m.be...@ufz.de>, www.ufz.de <http://www.ufz.de>
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
___
Please keep all replies on the list by using "reply all"
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[galaxy-dev] tabular data display
Dear list, I'm struggling with tabular data in Galaxy. Attached is a tab separated file that is generated by MetaProSIP (an updated - not yet committed -- version). The problem is that it is not shown as table in Galaxy (dev) at all. Also the peek preview is odd, some values of the header and data are omitted. Is this a bug in Galaxy, or of the data in the table? Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- #Peptide_Sequence Feature Quality_Report_Spectrum Quality_report_scores Sample_Name Protein_Accessions Description Unique #Ambiguity_members Score RT Exp._m/zTheo._m/z Charge TIC_fraction#non-natural_weightsPeak_intensitiesGroup Global_Peptide_LR RIA_1 LR_of_RIA_1 INT_1 Cor._1 RIA_2 LR_of_RIA_2 INT_2 Cor._2 RIA_3 LR_of_RIA_3 INT_3 Cor._3 RIA_4 LR_of_RIA_4 INT_4 Cor._4 RIA_5 LR_of_RIA_5 INT_5 Cor._5 RIA_6 LR_of_RIA_6 INT_6 Cor._6 RIA_7 LR_of_RIA_7 INT_7 Cor._7 RIA_8 LR_of_RIA_8 INT_8 Cor._8 RIA_9 LR_of_RIA_9 INT_9 Cor._9 RIA_10 LR_of_RIA_10INT_10 Cor._10 YGGAVDPTVLGGVK feature spectrum_dataset_3_J63R_rt_4831.43346884947.pdf scores_dataset_3_J63R_rt_4831.43346884947.pdf dataset_3.dat CONTIG23640_802236 length=2326__numreads=28_strand:-1_frame:0_orf_location:136:990 1 1 0.174659044235501 80.52 666.8623666.86152 0.831887919884232 7 659720_461384_165174_49177_14782_11728_6541_7410_10868_8404_9437_9556_10203_12619_12159_15831_16288_19847_19258_2_21275_21576_21294_22006_24019_19046_17493_19060_17884_15631_15769_13964_14131_10090_9445_9216_7297_6670_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0 0 0.269627132474428 0.6 1.0 1432378.6 1.0 36.50.0 146375.70.9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] argparse -> tool xml advice
Hi Helena,
yep, separate xml files would be fine. I was first thinking about a
single xml file having a select in the begin that allows to choose which
of the functionalities to use (eg one option per subparser). But I guess
the xml file might become quite large and unhandy.
Cheers,
Matthias
On 28.05.2018 11:12, H. Rasche wrote:
Hi Matthias,
On 2018-05-28, Matthias Bernt wrote:
Hi Helena,
got it running, but I struggling with subparsers (the tools that I try to
wrap basically only uses subparsers .. a lot of them). I adapted the
example.py in your repo to include a subparser which seems to be excluded
from the xml.
I call `python example.py --generate_galaxy_xml`
since `python example.py sub --generate_galaxy_xml` seems not to work.
Yeah, I never implemented support for subparsers. What sort of XML would
you expect that to output? I think, to me, it feels like it should
output multiple tool XMLs, one for each subparser.
Any suggestions?
Best,
Matthias
On 28.05.2018 10:02, H. Rasche wrote:
Hey Matthias,
And let me know if you have any questions or bugs!
There are a couple of things it won't do, but if you're looking to get
90% of the way from python script to tool interface, it will do that. It
won't get you the last 10% of nice repeat blocks and sections and all of
the things that help make galaxy tools more user-friendly. But this can
still be a huge time savings
Cheers,
Helena (@erasche)
On 2018-05-28, Björn Grüning wrote:
Hi Matthias,
check this one out: https://github.com/erasche/argparse2tool
Cheers,
Bjoern
Am 28.05.2018 um 09:43 schrieb Matthias Bernt:
Dear list,
just a question for advice: I plan to wrap a python script (with lots of
options) which uses the argparse library. I was wondering if somebody has
an idea to generate the tool xml (semi-)automatically? For instance, by
subclassing the formatter, parsing the python code, or parsing the command
line...
Cheers,
Matthias
___
Please keep all replies on the list by using "reply all"
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and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig
Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
# /usr/bin/python3
import argparse
parser = argparse.ArgumentParser(description='Process some integers.', prefix_chars='-+',
epilog="here's some epilog text",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('keyword', metavar='Q', type=str, nargs=1, help='action
keyword')
parser.add_argument('integers', metavar='N', type=int, nargs='+',
help='an integer for the accumulator')
parser.add_argument('--sum', '-s', dest='accumulate', action='store_const',
const=sum, default=max, help='sum the integers (default:
find the max)')
parser.add_argument('--foo', nargs='?', help='foo help')
parser.add_argument('--bar', nargs='*', default=[1, 2, 3], help='BAR!')
parser.add_argument('--true', action='store_true', help='Store a true')
parser.add_argument('--false', action='store_false', help='Store a false')
parser.add_argument('--append', action='append', help='Append a value')
parser.add_argument('--nargs2', nargs=2, help='nargs2')
parser.add_argument('--mode', choices=['rock', 'paper', 'scissors'],
default='scissors')
parser.add_argument('--version', action='version', version='2.0')
subparsers = parser.add_subparsers()
subparser = subparsers.add_parser('sub', help='test subparser')
subparser.add_argument('keyword', type=str)
subparser.add_argument('--subtrue', action='store_true', help='Store a true')
args = parser.parse_args()
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregiste
Re: [galaxy-dev] argparse -> tool xml advice
Hi Helena,
got it running, but I struggling with subparsers (the tools that I try
to wrap basically only uses subparsers .. a lot of them). I adapted the
example.py in your repo to include a subparser which seems to be
excluded from the xml.
I call `python example.py --generate_galaxy_xml`
since `python example.py sub --generate_galaxy_xml` seems not to work.
Any suggestions?
Best,
Matthias
On 28.05.2018 10:02, H. Rasche wrote:
Hey Matthias,
And let me know if you have any questions or bugs!
There are a couple of things it won't do, but if you're looking to get
90% of the way from python script to tool interface, it will do that. It
won't get you the last 10% of nice repeat blocks and sections and all of
the things that help make galaxy tools more user-friendly. But this can
still be a huge time savings
Cheers,
Helena (@erasche)
On 2018-05-28, Björn Grüning wrote:
Hi Matthias,
check this one out: https://github.com/erasche/argparse2tool
Cheers,
Bjoern
Am 28.05.2018 um 09:43 schrieb Matthias Bernt:
Dear list,
just a question for advice: I plan to wrap a python script (with lots of
options) which uses the argparse library. I was wondering if somebody has
an idea to generate the tool xml (semi-)automatically? For instance, by
subclassing the formatter, parsing the python code, or parsing the command
line...
Cheers,
Matthias
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
# /usr/bin/python3
import argparse
parser = argparse.ArgumentParser(description='Process some integers.', prefix_chars='-+', epilog="here's some epilog text", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('keyword', metavar='Q', type=str, nargs=1, help='action keyword')
parser.add_argument('integers', metavar='N', type=int, nargs='+',
help='an integer for the accumulator')
parser.add_argument('--sum', '-s', dest='accumulate', action='store_const',
const=sum, default=max, help='sum the integers (default: find the max)')
parser.add_argument('--foo', nargs='?', help='foo help')
parser.add_argument('--bar', nargs='*', default=[1, 2, 3], help='BAR!')
parser.add_argument('--true', action='store_true', help='Store a true')
parser.add_argument('--false', action='store_false', help='Store a false')
parser.add_argument('--append', action='append', help='Append a value')
parser.add_argument('--nargs2', nargs=2, help='nargs2')
parser.add_argument('--mode', choices=['rock', 'paper', 'scissors'], default='scissors')
parser.add_argument('--version', action='version', version='2.0')
subparsers = parser.add_subparsers()
subparser = subparsers.add_parser('sub', help='test subparser')
subparser.add_argument('keyword', type=str)
subparser.add_argument('--subtrue', action='store_true', help='Store a true')
args = parser.parse_args()
___
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Re: [galaxy-dev] argparse -> tool xml advice
Cool :) Thanks. Matthias On 28.05.2018 09:52, Björn Grüning wrote: Hi Matthias, check this one out: https://github.com/erasche/argparse2tool Cheers, Bjoern Am 28.05.2018 um 09:43 schrieb Matthias Bernt: Dear list, just a question for advice: I plan to wrap a python script (with lots of options) which uses the argparse library. I was wondering if somebody has an idea to generate the tool xml (semi-)automatically? For instance, by subclassing the formatter, parsing the python code, or parsing the command line... Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] argparse -> tool xml advice
Dear list, just a question for advice: I plan to wrap a python script (with lots of options) which uses the argparse library. I was wondering if somebody has an idea to generate the tool xml (semi-)automatically? For instance, by subclassing the formatter, parsing the python code, or parsing the command line... Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] fonts on headless compute nodes
Hi Nicola, thanks. That worked. Matthias On 25.04.2018 12:07, Nicola Soranzo wrote: Hi Matthias, if you add 'openjdk >8.0.121' to your conda command below, you should get openjdk from conda-forge. For an explanation, see: https://github.com/bioconda/bioconda-recipes/pull/8588 https://github.com/conda/conda/issues/6948#issuecomment-369360906 Cheers, Nicola On 25/04/18 10:44, Matthias Bernt wrote: Hi Bjoern, still struggling with your suggestion: > can you make sure FASTQC gets the openjdk version from conda-forge and > not from defaults? This will fix our one problem. conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --name __fastqc@0.11.5 fastqc=0.11.5 fastqc: 0.11.5-pl5.22.0_3 bioconda openjdk: 8.0.121-1 perl: 5.22.0.1-0 conda-forge removing --channel defaults still resulted in the same. Then I upgraded conda (4.3.27-py35h1706b01_0 --> 4.5.1-py35_0), and now at least removing the defaults channel has an effect .. but still openjdk is not installed from conda-forge (instead an ominous zulu jdk is installed from bioconda): fastqc: 0.11.5-1 bioconda java-jdk: 8.0.92-1 bioconda Any comments on this? Best, Matthias Am 11.04.2018 um 14:51 schrieb Matthias Bernt: Dear list, I found that some tools (eg FastQC and MetaProSIP) have problems with missing fonts (the former is java and the latter caused by R) on our compute nodes which do not have xorg and no fonts installed. On the cluster head nodes several font related packages are installed: dejavu-fonts-common-2.33-1.el6.noarch xorg-x11-fonts-Type1-7.2-11.el6.noarch liberation-fonts-common-1.05.1.20090721-5.el6.noarch liberation-sans-fonts-1.05.1.20090721-5.el6.noarch dejavu-sans-fonts-2.33-1.el6.noarch urw-fonts-2.4-11.el6.noarch ghostscript-fonts-5.50-23.2.el6.noarch xorg-x11-fonts-misc-7.2-11.el6.noarch It seems that conda no fonts are available. Is there somebody with similar problems. Any hint which of the packages is/are actually needed. Maybe our admins could install them... I also found for MetaProSIP that several xorg-... packages are needed. Should such dependencies be handled by the conda packages or by the Galaxy tool. Best, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] fonts on headless compute nodes
Hi Bjoern, still struggling with your suggestion: > can you make sure FASTQC gets the openjdk version from conda-forge and > not from defaults? This will fix our one problem. conda create -y --override-channels --channel iuc --channel bio conda --channel conda-forge --channel defaults --name __fastqc@0.11.5 fastqc=0.11.5 fastqc: 0.11.5-pl5.22.0_3 bioconda openjdk: 8.0.121-1 perl:5.22.0.1-0conda-forge removing --channel defaults still resulted in the same. Then I upgraded conda (4.3.27-py35h1706b01_0 --> 4.5.1-py35_0), and now at least removing the defaults channel has an effect .. but still openjdk is not installed from conda-forge (instead an ominous zulu jdk is installed from bioconda): fastqc: 0.11.5-1 bioconda java-jdk: 8.0.92-1 bioconda Any comments on this? Best, Matthias Am 11.04.2018 um 14:51 schrieb Matthias Bernt: Dear list, I found that some tools (eg FastQC and MetaProSIP) have problems with missing fonts (the former is java and the latter caused by R) on our compute nodes which do not have xorg and no fonts installed. On the cluster head nodes several font related packages are installed: dejavu-fonts-common-2.33-1.el6.noarch xorg-x11-fonts-Type1-7.2-11.el6.noarch liberation-fonts-common-1.05.1.20090721-5.el6.noarch liberation-sans-fonts-1.05.1.20090721-5.el6.noarch dejavu-sans-fonts-2.33-1.el6.noarch urw-fonts-2.4-11.el6.noarch ghostscript-fonts-5.50-23.2.el6.noarch xorg-x11-fonts-misc-7.2-11.el6.noarch It seems that conda no fonts are available. Is there somebody with similar problems. Any hint which of the packages is/are actually needed. Maybe our admins could install them... I also found for MetaProSIP that several xorg-... packages are needed. Should such dependencies be handled by the conda packages or by the Galaxy tool. Best, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] fonts on headless compute nodes
Dear list, I found that some tools (eg FastQC and MetaProSIP) have problems with missing fonts (the former is java and the latter caused by R) on our compute nodes which do not have xorg and no fonts installed. On the cluster head nodes several font related packages are installed: dejavu-fonts-common-2.33-1.el6.noarch xorg-x11-fonts-Type1-7.2-11.el6.noarch liberation-fonts-common-1.05.1.20090721-5.el6.noarch liberation-sans-fonts-1.05.1.20090721-5.el6.noarch dejavu-sans-fonts-2.33-1.el6.noarch urw-fonts-2.4-11.el6.noarch ghostscript-fonts-5.50-23.2.el6.noarch xorg-x11-fonts-misc-7.2-11.el6.noarch It seems that conda no fonts are available. Is there somebody with similar problems. Any hint which of the packages is/are actually needed. Maybe our admins could install them... I also found for MetaProSIP that several xorg-... packages are needed. Should such dependencies be handled by the conda packages or by the Galaxy tool. Best, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] environment for jobs
Dear list, there seem to be two ways to setup an environment for jobs: - in galaxy.ini: variable environment_setup_file - in job_conf.xml: tag in the destinations I'm wondering what the rationale is behind these two options? Is it to setup special environments for each destination? I guess that both should be loaded in each job. But in which order? I guessed that the file given in the tag is sourced in the job submit scripts, but this seems to happen not for all jobs...? Best, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] tool IO graph
Dear list, I started a little toy project (.. aka procrastination) that I would like to share here. It produces a graph connecting tool ids and input/output formats. As input it takes an arbitrary number of tool xml files https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tool-io-graph I could imagine some use cases: - could be nice for auto-generation of the documentation of a single tool (planemo?) - for tool suites one could easily check if the all tools are connected (I would expect this) - one could explore how tools could be plugged together, find out which tools generate a needed format currently it outputs dot formatted graphs. I can easily see some extensions - filter for subsets of tools / formats - get the surrounding of a tool (e.g. all nodes in distance 2, 4, ...) - filter paths from an available input to a desired output format Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] upload from dropbox
Hi Curtis, thanks for your comments. In addition I found out that wget works irrespective of the suffix. So setting the user agent might also help. I opened an issue and wait for some comments: https://github.com/galaxyproject/galaxy/issues/5330 Best, Matthias On 17.01.2018 20:38, Hendrickson, Curtis (Campus) wrote: Matthias, The default link generated by dropbox ends in http….?dl=0, which brings up a webpage with a download option. To get a direct download, change the suffix to ?dl=1 Perhaps you could even hack galaxy’s upload script to recognize these URLs and patch them on the fly - that would be a public service to us all. Example: View in a web page (default link generated by system right-click or other dropbox bits): _https://www.dropbox.com/s/lqsz785od3rxzhv/hello.txt?dl=0_ Download raw file: <https://www.dropbox.com/s/lqsz785od3rxzhv/hello.txt?dl=1>https://www.dropbox.com/s/lqsz785od3rxzhv/hello.txt?dl= <https://www.dropbox.com/s/ozr67t1yt378665/NetFlix French for Kids.docx?dl=1>1 I pasted this URL into usegalaxy.org <http://usegalaxy.org>, set data type to tabular, and it worked fine: https://usegalaxy.org/u/curtish-uab/h/dropboxcom-test Regards, Curtis On Jan 16, 2018, at 8:12 AM, Matthias Bernt <m.be...@ufz.de <mailto:m.be...@ufz.de>> wrote: Dear list and a happy new year, does anyone has experience with upload from dropbox to galaxy (by pasting the shared link)? I always get an empty dataset with the additional info "The uploaded file contains inappropriate HTML content". I guess the dropbox download link is not actually a real download link but a link to a website that contains some javascript button that starts the download... Best, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de <mailto:m.be...@ufz.de>, www.ufz.de <http://www.ufz.de> Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] upload from dropbox
Dear list and a happy new year, does anyone has experience with upload from dropbox to galaxy (by pasting the shared link)? I always get an empty dataset with the additional info "The uploaded file contains inappropriate HTML content". I guess the dropbox download link is not actually a real download link but a link to a website that contains some javascript button that starts the download... Best, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] tool publishing
Hi Marius,
Also there is a discrepancy between the `name` you're using in the
.shed.yml and the name as displayed in the
toolshed, that is probably another issue to look at.
That was the problem. Thanks a lot. Can the name of the owner be freely
chosen? I remember that I specified a username when registering, but I
could not remember (and could not find a way to find this information on
the toolshed page).
Best,
Matthias
On 18 December 2017 at 10:49, Matthias Bernt <m.be...@ufz.de> wrote:
Dear peter,
thanks for your comments. I tried to update:
`planemo shed_update --shed_target testtoolshed`
But planemo also complains about non existent repository:
```
Repository [fasta_regex_finder] does not exist in the targeted Tool Shed.
Failed to update repository 'fasta_regex_finder' as it does not exist on the
test Tool Shed
```
Cheers,
Matthias
On 18.12.2017 10:45, Peter Briggs wrote:
Hello Matthias
My reading of the planemo docs it was that "shed_create" just made the
repository, and that it had to be followed by the "shed_update" command in
order to upload the actual content. (The documentation could probably be
clearer on this I think.)
I'm not sure about the error from "shed_diff", maybe related to the
repository not having any content.
Best wishes
Peter
--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of
Matthias Bernt [m.be...@ufz.de]
Sent: Monday, December 18, 2017 9:37 AM
To: Galaxy Dev List
Subject: [galaxy-dev] tool publishing
Dear dev-list,
I'm just trying to publish my first tool to the testtoolshed via
planemo. I got some problem during the process. Maybe someone can
kickstart me (I guess I just forgot something).
I followed http://planemo.readthedocs.io/en/latest/publishing.html
The step
`planemo shed_create --shed_target testtoolshed`
```
Repository created
cd '/home/berntm/projects/mb-galaxy-tools/fasta_regex_finder' && git
rev-parse HEAD
cd '/home/berntm/projects/mb-galaxy-tools/fasta_regex_finder' && git
diff --quiet
Repository [fasta_regex_finder] does not exist in the targeted Tool Shed.
```
When I check online the repository is there but no changeset seems
available. Retrying fails (expected):
`planemo shed_create --shed_target testtoolshed`
```
Unexpected HTTP status code: 400: {"err_msg": "You already own a
repository named fasta_regex_finder<\/b>, please choose a different
name.", "err_code": 48}
Also shed_diff fails
`fasta_regex_finder git:(master) ✗ planemo shed_diff --shed_target
testtoolshed`
```
shed_diff: Repository [fasta_regex_finder] does not exist in the
targeted Tool Shed.
```
Any idea?
Cheers,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig
Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
___
Please keep all replies on the lis
[galaxy-dev] tool publishing
Dear dev-list,
I'm just trying to publish my first tool to the testtoolshed via
planemo. I got some problem during the process. Maybe someone can
kickstart me (I guess I just forgot something).
I followed http://planemo.readthedocs.io/en/latest/publishing.html
The step
`planemo shed_create --shed_target testtoolshed`
```
Repository created
cd '/home/berntm/projects/mb-galaxy-tools/fasta_regex_finder' && git
rev-parse HEAD
cd '/home/berntm/projects/mb-galaxy-tools/fasta_regex_finder' && git
diff --quiet
Repository [fasta_regex_finder] does not exist in the targeted Tool Shed.
```
When I check online the repository is there but no changeset seems
available. Retrying fails (expected):
`planemo shed_create --shed_target testtoolshed`
```
Unexpected HTTP status code: 400: {"err_msg": "You already own a
repository named fasta_regex_finder<\/b>, please choose a different
name.", "err_code": 48}
Also shed_diff fails
`fasta_regex_finder git:(master) ✗ planemo shed_diff --shed_target
testtoolshed`
```
shed_diff: Repository [fasta_regex_finder] does not exist in the
targeted Tool Shed.
```
Any idea?
Cheers,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/
Re: [galaxy-dev] intended behaviour for multiple data sets
Dear Jen, thanks for the detailed info. I was asking more from a tool developers perspective. But I found the answer: the multiple parameter of the input tag -- I forgot about it. Best, Matthias On 14.12.2017 21:40, Jennifer Hillman-Jackson wrote: Hello, How the data is consumed is explained on the tool form in the data entry area. Please review how to interpret this below and let us know if you are not sure about a particular tool. We might be able to explain how to access the help, or the tool might need an update to make the usage clearer. Example1: *Samtools Sort* > click on the Multiple Dataset or Dataset Collection icons and this new help text will be presented: This is a batch mode input field. Separate jobs will be triggered for each dataset selection. Example2: *Samtools Mpileup* > multiple dataset selection is the default (one or more can be chosen), or click to Collections where one or more can be selected. No new help text is presented to warn about the batch job mode. This means that inputs are processed together in the same job. More complex entry can be found on tools like *Compare two Datasets*, where there are two input sections and each can have a single or multiple (batch) entry (individually selected or in a collection). The batch mode help text comes up when multiple/collections are selected. This is expanded behavior similar to *Sort* above. And even more complex entry can be found on tools like *MultiQC*, where one or more input sets can be selected, and additional input sets (Reports) sections can be optionally added in. There is no batch mode entry text reported, meaning that all data is run with the same job. This is expanded behavior similar to *Mpileup* above, where each subsection is combined to produce a summary sub-report, then the final results from each sub-report is combined into the final report. *Galaxy tutorials: *https://galaxyproject.org/learn/ Hope that helps! Jen -- Jennifer Hillman-Jackson Galaxy Application Support http://usegalaxy.org http://galaxyproject.org http://biostar.usegalaxy.org On Thu, Dec 14, 2017 at 3:34 AM, Matthias Bernt <m.be...@ufz.de <mailto:m.be...@ufz.de>> wrote: Dear list, In addition to single datasets tool file inputs allow to choose between - multiple dataset - dataset collection - some tools use repeat tags for multiple inputs I would like to know what the intended behavior of galaxy is for the three options considering multiple datasets? Is this described somewhere? Is it that the tool is applied to each of the multiple inputs separately or at once. For some tools one case makes more sense than the other. Best, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany <https://maps.google.com/?q=Permoserstra%C3%9Fe+15,+04318+Leipzig,+Germany=gmail=g> Phone +49 341 235 482296 <tel:%2B49%20341%20235%20482296>, m.be...@ufz.de <mailto:m.be...@ufz.de>, www.ufz.de <http://www.ufz.de> Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/> To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/search/> -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Gesc
[galaxy-dev] tool dependencies
Hi all, I tried to install velvetoptimizer (for the assembly tutorial in the GTN). It lists velvetoptimiser as requirement in the main xml and the tool_dependencies.xml (listing the installation steps). Now there seems to be a conda package perl-velvetoptimiser. What would be the steps to to update the tool (I would happily create a PR)? Is the tool_dependencies.xml intended to be kept and I just need to update the names of the requirements (I guess the name in the tool_dependencies.xml does not matter)? Furthermore the tool_dependencies.xml includes the package_velvet which is listed as missing dependency in the management pages. Shouldn't this be ignored if there is a conda package? Last question: Is it possible to update an installed package by editing the xml files? It seemed to me that changes do not have an effect. Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] contribute to tools without github
I noticed that the sparql_uniprot tool does not run (python3 incompatibility). Since there is no github page I do not know how to contribute to such a tool. I have a similar problem with the lefse tool. What would be the best way to fix sich tools? Best, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] error despite success
Dear list,
today I got an erroneous result (red) despite the output of the tool to
be seems fine. Seemingly there was an error during setting the metadata.
```
Fatal error: An error occured during execution, see stderr and stdout
for more information
Reading reference gene model
/gpfs1/data/galaxy_server/galaxy-dev/database/files/002/dataset_2992.dat
... Done
Loading SAM/BAM file ... Finished
Total 62188 usable reads were sampled
Traceback (most recent call last):
File
"/gpfs1/data/galaxy_server/galaxy-dev/jobs_dir/001/1858/set_metadata_Ad6q_v.py",
line 1, in
from galaxy_ext.metadata.set_metadata import set_metadata;
set_metadata()
File
"/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy_ext/metadata/set_metadata.py",
line 85, in set_metadata
datatypes_registry.load_datatypes(root_dir=galaxy_root,
config=datatypes_config)
File
"/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/datatypes/registry.py",
line 109, in load_datatypes
tree = galaxy.util.parse_xml(config)
File
"/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/util/__init__.py", line
214, in parse_xml
root = tree.parse(fname,
parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget()))
File
"/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/xml/etree/ElementTree.py",
line 647, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory:
'/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp_uHZbW'
```
Are there any suggestions how to continue with such a behavior. The file
system on our cluster seems to be slow at the moment, could this be the
cause?
Best,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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[galaxy-dev] another conda problem
Dear list, thanks for giving me a workaround for yesterdays conda problem. Today I got a new one: I tried to install RSeQC which installs (including the dependencies) without reporting an error in the galaxy admin UI. But actually the package is not installed, e.g. infer_experiment.py can not be found in the environment. When I check the galaxy logs I find the following: `Installing conda-forge::wheel-0.30.0-py_1 requires a minimum conda version of 4.3.` Can I safely update conda to version 4.3? Galaxy's conda FAQ https://docs.galaxyproject.org/en/master/admin/conda_faq.html suggests 4.2.13? Is the successful reporting of the installation a bug? Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] conda bash environment problem as real user
Dear list, our galaxy runs jobs as real user and I get the following error for multiple tools: """ Failed to activate conda environment! Error was: CondaEnvironmentError: Environment error: Cannot activate environment bash. User does not have write access for conda symlinks. Fatal error: Exit code 1 () """ Does anyone have an idea where I could start digging? My workaround (run the tool once as galaxy user) is to time consuming since I have to restart galaxy 2x. Thanks a lot. Cheers, Matthias P.S.: https://github.com/galaxyproject/galaxy/issues/4767 -- ------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] resubmission on out of memory
Dear list, I recall that its possible to configure a tool can such that out of memory conditions (and run time) can be recognized (by regexp matching on stadout/stderr). Can this be used to trigger job resubmission on the cluster? Could someone please point me to some kind of documentation, if this is the case? Best, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] galaxy behind firewall
Hi, our galaxy is behind a firewall which seems to imply that many of the nice possibilities to use online services which download data from galaxy do not work, e.g. phinch or the UCSC browser. Has anybody ideas for (or experience with) workarounds? Maybe you can elaborate about these firewall issues first ? What do you mean by "do not work" ? Did you get in touch with your security team ? For instance, biom files can be visualised at phinch. If a user clicks the link "view biom at Phinch" a new website is opened: http://www.bx.psu.edu/~dan/Phinch/index.html?biomURL=http%3A%2F%2Fbioinf2-dev%3A8080%2Fdisplay_application%2F7aee12da589cb4d4%2Fbiom_simple%2Fphinch_dan%2F772601c34b88e564%2Fdata%2Fgalaxy_7aee12da589cb4d4.biom so the phinch website tries to download the biom file from our local Galaxy bioinf2-dev which is behind the firewall. Similar mechanism is at work to visualize annotations at the UCSC genome browser. There is no way that our security team will open the firewall for galaxy which runs on a head node of our compute cluster. For instance, we have a local own cloud which we might exploit, i.e., upload the data to OC and modify the link. What kind of integration are you intending with ownCloud exactly ? I was just thinking that one could create a tool that uploads the data set to OC, makes it publicly accessible via a link, and redirects to a website (essentially replacing the link to the galaxy by the one to OC). Cheers, Matthias ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] galaxy behind firewall
Dear list, our galaxy is behind a firewall which seems to imply that many of the nice possibilities to use online services which download data from galaxy do not work, e.g. phinch or the UCSC browser. Has anybody ideas for (or experience with) workarounds? For instance, we have a local own cloud which we might exploit, i.e., upload the data to OC and modify the link. Best, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] tool runtimes
Dear list, I have the impression that on our cluster the "auxiliary" computations (e.g. setting metadata) is very slow (minutes) compared to the run time of the actual tools (often just seconds). Do you have any suggestion how I can tweak this or how I can analyze this more detailed? Best, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] installation/conda problems
Dear list, I think I have messed up the environment for one tool (IntaRNA) -- can someone tell me what to do to get a clear environment? Here is what happened. I have started the installation (via ansible) and accidentally aborted it. Then the tool gave me the following error: ``` Failed to activate conda environment! Error was: CondaEnvironmentError: Environment error: Cannot activate environment bash. User does not have write access for conda symlinks. Fatal error: Exit code 1 (Error occurred. Please check Tool Standard Error) ``` Since uninstalling and reinstallation (via ansible) gave the same result I tried to reinstall from the Galaxy UI. Now I got (even if if the admin interface list the tool as installed): ``` Fatal error: Exit code 127 (Error occurred. Please check Tool Standard Error) /gpfs1/data/galaxy_server/galaxy-dev/jobs_dir/000/362/tool_script.sh: line 25: IntaRNA: command not found ``` Is there a list of directories and files that I could clear to get rid of any trace of the tool and start anew? Best, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] conda problem
Hi Bjoern, thanks for the information. Then I will check for a new version next week and check if the problem is gone. Have a great weekend. Cheers, Matthias On 31.08.2017 18:24, Björn Grüning wrote: Hi Matthias, conda-build only supported 80 chars limit for a long time. This has fixed and all new packages don't have this problem. So hopefully this PR will fix it: https://github.com/bioconda/bioconda-recipes/pull/5912 Cheers, bjeorn On 31.08.2017 17:19, Matthias Bernt wrote: Dear list, When running rmarkdown_wgcna I get the following error in the logs: PaddingError: Placeholder of length '80' too short in package bioconda::r-wgcna-1.51-r3.3.1_0. The package must be rebuilt with conda-build > 2.0. The command that seems to lead to this is: Executing command: /gpfs1/data/galaxy_server/galaxy-dev/database/dependencies/_conda/bin/conda create -y --name mulled-v1-3bfe8da4ed798836281cc963619917 317ae960c9a828f7ea05d1670c65b19619 pandoc=1.15.0.6-0 r-getopt=1.20.0 r-rmarkdown=1.2 r-plyr=1.8.4 r-highcharter=0.4.0 r-dt=0.2 r-htmltools=0.3.5 r-wgcna=1.51 Any ideas? Best, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] unipept visualization
Hi Sam, I tried on 17.05 and dev without any success. Any idea where I could start debugging? Best, Matthias On 30.08.2017 18:23, Aysam Guerler wrote: Hey Matthias, I noticed that this visualization has already been added and should be working in release 17.05 and a d3_hierarchy file. Its documented at https://github.com/galaxyproject/galaxy/tree/dev/config/plugins/visualizations/unipept. Example files are available here: https://github.com/unipept/unipept-visualizations/tree/master/examples/data Now here is the issue I noticed, once you upload one of these example files, you need to select the file in the history, click on the pencil icon and change the datatype to 'd3_hierarchy' before attempting to visualize it. You cannot select the correct datatype in the upload view. I will test this a little bit more and fix it if necessary for the next release. I hope this helps. Thanks again. On Mon, Aug 28, 2017 at 4:23 AM, Matthias Bernt <m.be...@ufz.de <mailto:m.be...@ufz.de>> wrote: Hi Sam, thanks for the answer. So far I have not configured anything, I was hoping that it works out of the box :). Could you point me to some documentation where the setup is explained? Best, Matthias On 25.08.2017 19 <tel:25.08.2017%2019>:05, Aysam Guerler wrote: Hi Matthias, Have you added the visulization to Charts or the regular Galaxy visualization framework? If it is the latter please make sure that you correctly specified the datatype in your XML file. Your visualization should than appear in the drop-down list in the history. Thanks, Sam On Fri, Aug 25, 2017 at 5:25 AM, Matthias Bernt <m.be...@ufz.de <mailto:m.be...@ufz.de> <mailto:m.be...@ufz.de <mailto:m.be...@ufz.de>>> wrote: Dear list, I can not get the wonderful unipept visualization to work on our Galaxy instance (a test instance on the dev branch). I get the message: "Unfortunately we could not identify a suitable plugin" The file I try to visualize was generated by unipept (pept2lca) and is of format d3_hierarchy. Could someone tell me if I need to install / configure something to get this running? Thanks a lot. Best, Matthias P.S. This might be also of interest for others, since this visualization is used in the Metaproteomics tutorial of the GTN. -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296 <tel:%2B49%20341%20235%20482296> <tel:%2B49%20341%20235%20482296>, m.be...@ufz.de <mailto:m.be...@ufz.de> <mailto:m.be...@ufz.de <mailto:m.be...@ufz.de>>, www.ufz.de <http://www.ufz.de> <http://www.ufz.de> Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/> <https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>> To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/search/> <http://galaxyproject.org/search/ <http://galaxyproject.org/search/>> -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15,
[galaxy-dev] conda problem
Dear list, When running rmarkdown_wgcna I get the following error in the logs: PaddingError: Placeholder of length '80' too short in package bioconda::r-wgcna-1.51-r3.3.1_0. The package must be rebuilt with conda-build > 2.0. The command that seems to lead to this is: Executing command: /gpfs1/data/galaxy_server/galaxy-dev/database/dependencies/_conda/bin/conda create -y --name mulled-v1-3bfe8da4ed798836281cc963619917 317ae960c9a828f7ea05d1670c65b19619 pandoc=1.15.0.6-0 r-getopt=1.20.0 r-rmarkdown=1.2 r-plyr=1.8.4 r-highcharter=0.4.0 r-dt=0.2 r-htmltools=0.3.5 r-wgcna=1.51 Any ideas? Best, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] galaxy-dev Digest, Vol 134, Issue 19
Dear ..., what are the file permissions for the file and the folder? Is the drmaa_external_runner.py python script run with sudo? Which release/branch are you on? Best, Matthias We are setting up run as real user but have run into a strange issue. When the drmaa external script is called it could not load the job json file. All permissions are set properly and the file exists. Upon attempting to run the script by itself this error is created. When loading a test script to open a file there is no issue. If the drmaa external script is run as root the same issue occurs. /mnt/ceph/home/galaxy/galaxy/files_directory/database/slurm/11.jt_json Traceback (most recent call last): File "scripts/drmaa_external_runner.py", line 157, in main() File "scripts/drmaa_external_runner.py", line 146, in main load_job_template_from_file(jt, json_filename) File "scripts/drmaa_external_runner.py", line 43, in load_job_template_from_file f = open(filename, 'r') IOError: [Errno 13] Permission denied: '/mnt/ceph/home/galaxy/galaxy/files_directory/database/slurm/11.jt_json' ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] unipept visualization
Hi Sam, thanks for the answer. So far I have not configured anything, I was hoping that it works out of the box :). Could you point me to some documentation where the setup is explained? Best, Matthias On 25.08.2017 19:05, Aysam Guerler wrote: Hi Matthias, Have you added the visulization to Charts or the regular Galaxy visualization framework? If it is the latter please make sure that you correctly specified the datatype in your XML file. Your visualization should than appear in the drop-down list in the history. Thanks, Sam On Fri, Aug 25, 2017 at 5:25 AM, Matthias Bernt <m.be...@ufz.de <mailto:m.be...@ufz.de>> wrote: Dear list, I can not get the wonderful unipept visualization to work on our Galaxy instance (a test instance on the dev branch). I get the message: "Unfortunately we could not identify a suitable plugin" The file I try to visualize was generated by unipept (pept2lca) and is of format d3_hierarchy. Could someone tell me if I need to install / configure something to get this running? Thanks a lot. Best, Matthias P.S. This might be also of interest for others, since this visualization is used in the Metaproteomics tutorial of the GTN. -- ------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296 <tel:%2B49%20341%20235%20482296>, m.be...@ufz.de <mailto:m.be...@ufz.de>, www.ufz.de <http://www.ufz.de> Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/> To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/search/> -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] unipept visualization
Dear list, I can not get the wonderful unipept visualization to work on our Galaxy instance (a test instance on the dev branch). I get the message: "Unfortunately we could not identify a suitable plugin" The file I try to visualize was generated by unipept (pept2lca) and is of format d3_hierarchy. Could someone tell me if I need to install / configure something to get this running? Thanks a lot. Best, Matthias P.S. This might be also of interest for others, since this visualization is used in the Metaproteomics tutorial of the GTN. -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] toolshed and testtoolshed
Dear dev-list, Bjoern Gruening was so nice to provide a fix for one of the galaxy tools (openms_metaprosip). It seems that the fix found its way into the testtoolshed, but not the toolshed. So I was curious how the connection between these two tool sources works. - Is there a regular sync interval? Or does someone need to push a button to get a new version to the toolshed? - Are the versions (and the hashes) of the tools that find their way to the main toolshed identical? Then I could just switch the tool_shed_url in my tool_list.yml file when the desired version or a newer one appears in the main toolshed. - I guess its not a good idea (in general) to provide tools from the testtoolshed in a prodiction instance? Best, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] Galaxy Conda resolver install Issue
Hi Evan, just for completeness Marius is referring to these changes: https://github.com/galaxyproject/galaxy/pull/4049 For testing you could also integrate these changes in your instance, but upgrading to an up-to-date version is a good idea anyways. Best, Matthias Hello Evan, this looks suspiciously like a bug that Matthias Bernt has fixed on the development branch a while back. I have backported this to Galaxy release 17.01 and release 17.05. If you update your galaxy branch to the latest commit it should work (or you should receive a more instructive error message). Hope that helps, Marius On 17 August 2017 at 18:32, evan clark <eclar...@fau.edu> wrote: I just ran across an issue when attempting to load galaxy. I am not sure how to fix this issue or what could be causing it. Conda is installed properly. File "/var/web_services/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 58, in paste_app_factory app = galaxy.app.UniverseApplication( global_conf=global_conf, **kwargs ) File "/var/web_services/galaxy/lib/galaxy/app.py", line 113, in __init__ self._configure_toolbox() File "/var/web_services/galaxy/lib/galaxy/config.py", line 935, in _configure_toolbox self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) File "/var/web_services/galaxy/lib/galaxy/tools/__init__.py", line 205, in __init__ app=app, File "/var/web_services/galaxy/lib/galaxy/tools/toolbox/base.py", line 1044, in __init__ self._init_dependency_manager() File "/var/web_services/galaxy/lib/galaxy/tools/toolbox/base.py", line 1057, in _init_dependency_manager self.dependency_manager = build_dependency_manager( self.app.config ) File "/var/web_services/galaxy/lib/galaxy/tools/deps/__init__.py", line 41, in build_dependency_manager dependency_manager = DependencyManager( **dependency_manager_kwds ) File "/var/web_services/galaxy/lib/galaxy/tools/deps/__init__.py", line 84, in __init__ self.dependency_resolvers = self.__build_dependency_resolvers( conf_file ) File "/var/web_services/galaxy/lib/galaxy/tools/deps/__init__.py", line 193, in __build_dependency_resolvers return self.__default_dependency_resolvers() File "/var/web_services/galaxy/lib/galaxy/tools/deps/__init__.py", line 201, in __default_dependency_resolvers CondaDependencyResolver(self), File "/var/web_services/galaxy/lib/galaxy/tools/deps/resolvers/conda.py", line 134, in __init__ self.disabled = not galaxy.tools.deps.installable. ensure_installed(conda_context, install_conda, self.auto_init) File "/var/web_services/galaxy/lib/galaxy/tools/deps/installable.py", line 77, in ensure_installed return ensure_installed(installable_context, auto_init) TypeError: ensure_installed() takes exactly 3 arguments (2 given) ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] openms python3 & print
Hi Nicola and Bjoern, thanks a lot for the informations. I'm just installing the suite. Best, Matthias On 10.08.2017 16:08, Nicola Soranzo wrote: Hi Matthias, I think you're using an old version of the tool, the one at https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_decoydatabase/178e00cf12d7 doesn't use a Python wrapper. The development repository is at https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms Cheers, Nicola On 10/08/17 14:03, Matthias Bernt wrote: Hi, I got an error from OpenMS which seems to be related to python3: Fatal error: Exit code 1 (Error running OpenMS tool.) File "/gpfs1/data/galaxy_server/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/galaxyp/openms/42b843627623/openms/openms_wrapper.py", line 22 print "Running shell command %s" % command ^ SyntaxError: Missing parentheses in call to 'print' Command line was python /gpfs1/data/galaxy_server/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/galaxyp/openms/42b843627623/openms/openms_wrapper.py --executable 'DecoyDatabase' --config /gpfs1/data/galaxy_server/galaxy/jobs_dir/000/240/tmpYOuUf9 I would volunteer to improve this. But where can I find the sources? Would it be better to - use the compatibility import (easiest) - switch to print() - use logging Best, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] openms again
Hi,
just fixed the print() issue locally and ran into the next problems
which were easy to fix:
- ConfigParser -> configparser
- iteritems -> items
(The modified sources are attached if they are of interest)
Now I have an error that seems to be deeper:
Failed to find specific OpenMS option [shuffle] in node [at 0x2b96a3b1c048>]
Any ideas?
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
import os
import sys
from optparse import OptionParser
from configparser import SafeConfigParser
from xml.etree import ElementTree
import subprocess
from re import compile
DEBUG = False
def main():
(options, args) = _parse_args()
for executable, config_path in zip(options.executables, options.configs):
command_handler = COMMAND_HANDLERS.get(executable, _run_openms)
command_handler(executable, config_path)
def _run_shell(executable, config_path):
command = open(config_path, "r").read().strip()
if DEBUG:
print( "Running shell command %s" % command)
_exec(command)
def _run_openms(executable, config_path):
_exec("%s -write_ini openms.ini" % executable)
tree = ElementTree.parse("openms.ini")
options = _load_options(config_path)
_set_options(tree, executable, options)
tree.write("openms.ini")
if DEBUG:
print('With openms.ini as:\n%s\n, calling: %s -ini openms.ini' % (open("openms.ini", "r").read(), executable))
_exec("%s -ini openms.ini" % executable)
COMMAND_HANDLERS = {
"__SHELL__": _run_shell,
}
def _fail(message, return_code=1):
print( message )
sys.exit(return_code)
def _exec(command):
proc = subprocess.Popen(args=command, shell=True)
return_code = proc.wait()
if return_code != 0:
_fail("Error executing command [%s], return code is %d" % (command, return_code), return_code)
def _set_options(tree, executable, options):
executable_node = tree.find("./NODE[@name='%s']" % executable)
if executable_node is None:
_fail("Could not find options for executable %s" % executable)
options_node = executable_node.find("./NODE[@name='1']")
for key, raw_value in options.items("simple_options"):
if raw_value is None:
_fail("No value found key %s" % key)
value = _parse_value(raw_value)
_set_option(options_node, key.split("!"), value)
_set_option(options_node, ["no_progress"], "true", required=False)
def _set_option(node, key_parts, value, required=True):
key = key_parts[0]
if len(key_parts) == 1:
if not _set_item_value(node, key, value) and \
not _set_list_item_value(node, key, value) and \
required:
_fail("Failed to find specific OpenMS option [%s] in node [%s]" % (key, node))
else:
if node is None:
_fail("Failed to find specific OpenMS option [%s] in node [%s]" % (key, node))
sub_node = node.find("./NODE[@name='%s']" % key)
if sub_node is None:
_fail("Failed to find node for key %s" % key)
_set_option(sub_node, key_parts[1:], value, required)
def _set_item_value(node, key, value):
item = node.find("./ITEM[@name='%s']" % key)
if item is not None:
item.set("value", value)
return item is not None
def _set_list_item_value(node, key, values):
item = node.find("./ITEMLIST[@name='%s']" % key)
if item is not None:
for value in values.split(","):
ElementTree.SubElement(item, "LISTITEM", {"value": value})
return item is not None
def _parse_value(raw_value):
value = raw_value
for pattern, function in VALUE_FUNCTIONS.items():
try:
match = pattern.match(value)
except TypeError:
print( "Invalid value found config file %s" % value )
sys.exit(1)
if match:
value = function(*match.groups())
if value is None:
print( "Failed to properly parse raw value %s&q
[galaxy-dev] openms python3 & print
Hi, I got an error from OpenMS which seems to be related to python3: Fatal error: Exit code 1 (Error running OpenMS tool.) File "/gpfs1/data/galaxy_server/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/galaxyp/openms/42b843627623/openms/openms_wrapper.py", line 22 print "Running shell command %s" % command ^ SyntaxError: Missing parentheses in call to 'print' Command line was python /gpfs1/data/galaxy_server/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/galaxyp/openms/42b843627623/openms/openms_wrapper.py --executable 'DecoyDatabase' --config /gpfs1/data/galaxy_server/galaxy/jobs_dir/000/240/tmpYOuUf9 I would volunteer to improve this. But where can I find the sources? Would it be better to - use the compatibility import (easiest) - switch to print() - use logging Best, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] numpy problem
Dear dev-list,
here an answer to my own question.
The problem was that the tool "Group data by a column and perform
aggregate operation on other columns." returned an error:
Traceback (most recent call last): File
"/gpfs1/data/galaxy_server/galaxy-dev/tools/stats/grouping.py", line 15,
in import numpy ImportError: No module named numpy
So I thought that numpy is not installed. But the problem was that for
running the tool on a cluster the venv needs to be specified in
job_conf.xml, as documented here:
https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html#galaxy-job-handlers
Two follow up questions:
- Is it worth to extend the documentation on
https://galaxyproject.org/admin/config/performance/cluster/ or did I
just miss something? Does this apply for all remote runners?
- Is it possible to have the tag applied to multiple destinations,
eg by adding it to the instead of to ?
Cheers,
Matthias
On 18.07.2017 17:14, Matthias Bernt wrote:
Dear dev-list,
again some problems with software in galaxy: I can not get numpy to
install.
Here is the excerpt from the logs:
Successfully downloaded from url:
https://depot.galaxyproject.org/software/numpy/numpy_1.9p1_src_all.tar.gz
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,264 +
export
PYTHONPATH=$PYTHONPATH:/gpfs1/data/galaxy_server/galaxy/database/dependencies/numpy/1.9/iuc/package_numpy_1_9/83d12e13dbbd/lib/python
&&
export ATLAS=$ATLAS_ROOT_PATH &&
python setup.py install --install-lib
/gpfs1/data/galaxy_server/galaxy/database/dependencies/numpy/1.9/iuc/package_numpy_1_9/83d12e13dbbd/lib/python
--install-scripts
/gpfs1/data/galaxy_server/galaxy/database/dependencies/numpy/1.9/iuc/package_numpy_1_9/83d12e13dbbd/bin
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,384 Writing custom site.cfg for ATLAS in Galaxy
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,385 Traceback (most recent call last):
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,385 File "setup.py", line 264, in
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,385 setup_package()
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,385 File "setup.py", line 210, in setup_package
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,385 raise RuntimeError("Writing custom
site.cfg failed! %s" % ex)
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,385 RuntimeError: Writing custom site.cfg
failed! 'ATLAS_LIB_DIR'
I need this tool for running: "Group data by a column and perform
aggregate operation on other columns." which gives me currently a numpy
error:
Traceback (most recent call last): File
"/gpfs1/data/galaxy_server/galaxy/tools/stats/grouping.py", line 15, in
import numpy ImportError: No module named numpy
Thanks a lot.
Cheers,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/
[galaxy-dev] numpy problem
Dear dev-list,
again some problems with software in galaxy: I can not get numpy to
install.
Here is the excerpt from the logs:
Successfully downloaded from url:
https://depot.galaxyproject.org/software/numpy/numpy_1.9p1_src_all.tar.gz
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,264 +
export
PYTHONPATH=$PYTHONPATH:/gpfs1/data/galaxy_server/galaxy/database/dependencies/numpy/1.9/iuc/package_numpy_1_9/83d12e13dbbd/lib/python
&&
export ATLAS=$ATLAS_ROOT_PATH &&
python setup.py install --install-lib
/gpfs1/data/galaxy_server/galaxy/database/dependencies/numpy/1.9/iuc/package_numpy_1_9/83d12e13dbbd/lib/python
--install-scripts
/gpfs1/data/galaxy_server/galaxy/database/dependencies/numpy/1.9/iuc/package_numpy_1_9/83d12e13dbbd/bin
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,384 Writing custom site.cfg for ATLAS in Galaxy
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,385 Traceback (most recent call last):
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,385 File "setup.py", line 264, in
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,385 setup_package()
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,385 File "setup.py", line 210, in setup_package
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,385 raise RuntimeError("Writing custom
site.cfg failed! %s" % ex)
tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
DEBUG 2017-07-18 17:08:29,385 RuntimeError: Writing custom site.cfg
failed! 'ATLAS_LIB_DIR'
I need this tool for running: "Group data by a column and perform
aggregate operation on other columns." which gives me currently a numpy
error:
Traceback (most recent call last): File
"/gpfs1/data/galaxy_server/galaxy/tools/stats/grouping.py", line 15, in
import numpy ImportError: No module named numpy
Thanks a lot.
Cheers,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/
Re: [galaxy-dev] tool and planemo problems
Perfect. Thanks a lot. Maybe one could add a note to planemo --help that command specific help can be obtained with planemo command --help. Best, Matthias On 12.07.2017 16:57, Peter Cock wrote: Try: planemo lint --fail_level error sleepwaste.xml The default is to fail if there are warnings. Peter On Wed, Jul 12, 2017 at 3:55 PM, Matthias Bernt <m.be...@ufz.de> wrote: Hi Peter, I just call planemo l sleepwaste.xml Best, Matthias On 12.07.2017 16:54, Peter Cock wrote: How are you running planemo lint - in particular is it set to fail if there are any warnings present (like your missing citation warning)? Peter On Wed, Jul 12, 2017 at 3:52 PM, Matthias Bernt <m.be...@ufz.de> wrote: Dear list, In order to test the job resubmission feature I wrote a little tool for galaxy that just wastes a specified (minimum) time and memory (using different programming languages) for testing the new DRMAA job runner that I wrote. When linting it with planemo seemingly all tests are successful, but in the end I still get a fail -- verbose mode is also of no help here. Applying linter tests... CHECK .. CHECK: 7 test(s) found. Applying linter output... CHECK .. INFO: 1 outputs found. Applying linter inputs... CHECK .. INFO: Found 3 input parameters. Applying linter help... CHECK .. CHECK: Tool contains help section. .. CHECK: Help contains valid reStructuredText. Applying linter general... CHECK .. CHECK: Tool defines a version [0.1.0]. .. CHECK: Tool defines a name [Waste time and memory]. .. CHECK: Tool defines an id [sleepwaste]. .. CHECK: Tool targets 16.01 Galaxy profile. Applying linter command... CHECK .. INFO: Tool contains a command. Applying linter citations... WARNING .. WARNING: No citations found, consider adding citations to your tool. Applying linter tool_xsd... CHECK .. INFO: File validates against XML schema. Failed linting The test of the tool are all successful. Any ideas what is wrong? Once the problems are solved, would such a tool also be useful in the toolshed? Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ -- ------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- -- ------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your
Re: [galaxy-dev] tool and planemo problems
Hi Peter, I just call planemo l sleepwaste.xml Best, Matthias On 12.07.2017 16:54, Peter Cock wrote: How are you running planemo lint - in particular is it set to fail if there are any warnings present (like your missing citation warning)? Peter On Wed, Jul 12, 2017 at 3:52 PM, Matthias Bernt <m.be...@ufz.de> wrote: Dear list, In order to test the job resubmission feature I wrote a little tool for galaxy that just wastes a specified (minimum) time and memory (using different programming languages) for testing the new DRMAA job runner that I wrote. When linting it with planemo seemingly all tests are successful, but in the end I still get a fail -- verbose mode is also of no help here. Applying linter tests... CHECK .. CHECK: 7 test(s) found. Applying linter output... CHECK .. INFO: 1 outputs found. Applying linter inputs... CHECK .. INFO: Found 3 input parameters. Applying linter help... CHECK .. CHECK: Tool contains help section. .. CHECK: Help contains valid reStructuredText. Applying linter general... CHECK .. CHECK: Tool defines a version [0.1.0]. .. CHECK: Tool defines a name [Waste time and memory]. .. CHECK: Tool defines an id [sleepwaste]. .. CHECK: Tool targets 16.01 Galaxy profile. Applying linter command... CHECK .. INFO: Tool contains a command. Applying linter citations... WARNING .. WARNING: No citations found, consider adding citations to your tool. Applying linter tool_xsd... CHECK .. INFO: File validates against XML schema. Failed linting The test of the tool are all successful. Any ideas what is wrong? Once the problems are solved, would such a tool also be useful in the toolshed? Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] tool and planemo problems
Dear list, In order to test the job resubmission feature I wrote a little tool for galaxy that just wastes a specified (minimum) time and memory (using different programming languages) for testing the new DRMAA job runner that I wrote. When linting it with planemo seemingly all tests are successful, but in the end I still get a fail -- verbose mode is also of no help here. Applying linter tests... CHECK .. CHECK: 7 test(s) found. Applying linter output... CHECK .. INFO: 1 outputs found. Applying linter inputs... CHECK .. INFO: Found 3 input parameters. Applying linter help... CHECK .. CHECK: Tool contains help section. .. CHECK: Help contains valid reStructuredText. Applying linter general... CHECK .. CHECK: Tool defines a version [0.1.0]. .. CHECK: Tool defines a name [Waste time and memory]. .. CHECK: Tool defines an id [sleepwaste]. .. CHECK: Tool targets 16.01 Galaxy profile. Applying linter command... CHECK .. INFO: Tool contains a command. Applying linter citations... WARNING .. WARNING: No citations found, consider adding citations to your tool. Applying linter tool_xsd... CHECK .. INFO: File validates against XML schema. Failed linting The test of the tool are all successful. Any ideas what is wrong? Once the problems are solved, would such a tool also be useful in the toolshed? Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- sleepwaste.tar.bz2 Description: application/bzip ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] Improved DRMAAJobRunner (Peter van Heusden)
Hi Peter, FYI: just found on the galaxy documentation a paragraph that even recommends running upload on the cluster: https://galaxyproject.org/admin/config/performance/cluster/ """ If your cluster nodes have Internet access (NAT is okay) and you want to run the data source tools (upload, ucsc, etc.) on the cluster (doing so is highly recommended), set new_file_path in galaxy.ini to a directory somewhere in your shared filesystem: """ Cheers, Matthias On 10.07.2017 11:11, Matthias Bernt wrote: Dear Peter, my job_conf.xml is attached. Best, Matthuas On 08.07.2017 18:00, galaxy-dev-requ...@lists.galaxyproject.org wrote: Send galaxy-dev mailing list submissions to galaxy-dev@lists.galaxyproject.org To subscribe or unsubscribe via the World Wide Web, visit https://lists.galaxyproject.org/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-requ...@lists.galaxyproject.org You can reach the person managing the list at galaxy-dev-ow...@lists.galaxyproject.org When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..." HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. Re: any introduce for how Mako and JavaScript work ingalaxy? (Daniel Blankenberg) 2. Re: ustacks - bad interpreter (Björn Grüning) 3. Re: Improved DRMAAJobRunner (Peter van Heusden) (Matthias Bernt) 4. Re: Improved DRMAAJobRunner (Peter van Heusden) (Peter van Heusden) -- Message: 1 Date: Thu, 6 Jul 2017 22:36:27 -0400 From: Daniel Blankenberg <dan.blankenb...@gmail.com> To: Steven Shen <ishenwei...@gmail.com> Cc: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] any introduce for how Mako and JavaScript work ingalaxy? Message-ID: <CAE9nRFg+Edj2=3+K=6+FZCxj5=hb4togw+lm++e+sd1+j2+...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Steven, For a quick first pass, have you taken a look at https://github.com/ galaxyproject/galaxy/blob/dev/client/README.md? Thanks for using Galaxy, Dan On Thu, Jul 6, 2017 at 10:11 PM, Steven Shen <ishenwei...@gmail.com> wrote: Hi everyone, I want to make some change for my local galaxy web, actually I can edit galaxy_path/static/scripts/bundled/*.js directly. It seems mako templates are used for galaxy, as well as many JavaScript files, but I don't know how they work. So is there any introduce for how mako and JavaScript files working in galaxy? Thank you very much. Steven ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ -- next part -- An HTML attachment was scrubbed... URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20170706/8fbd5cbe/attachment-0001.html> -- Message: 2 Date: Sat, 8 Jul 2017 11:31:31 +0200 From: Björn Grüning <bjoern.gruen...@gmail.com> To: David Meltzer <david.melt...@glasgow.ac.uk>, Nate Coraor <n...@bx.psu.edu> Cc: "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyproject.org> Subject: Re: [galaxy-dev] ustacks - bad interpreter Message-ID: <a5a7d281-6040-f65e-e674-6cb2e9343...@gmail.com> Content-Type: text/plain; charset=utf-8 Hi, please also make sure you have a recent conda version. This 80 character length smalls a lot like an old conda restriction. Cheers, Bjoern Am 07.07.2017 um 18:09 schrieb David Meltzer: Good afternoon, Thank you for that! I will look in to it! Best Regards, David Jacob Meltzer *From: *Nate Coraor <n...@bx.psu.edu> *Date: *Friday, July 7, 2017 at 5:02 PM *To: *David Meltzer <david.melt...@glasgow.ac.uk> *Cc: *Yvan Le Bras <yvan.le-b...@mnhn.fr>, "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyproject.org> *Subject: *Re: [galaxy-dev] ustacks - bad interpreter Hi David, You may want to have a look at the first line of: /home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d
Re: [galaxy-dev] Improved DRMAAJobRunner (Peter van Heusden)
Dear Peter, my job_conf.xml is attached. Best, Matthuas On 08.07.2017 18:00, galaxy-dev-requ...@lists.galaxyproject.org wrote: Send galaxy-dev mailing list submissions to galaxy-dev@lists.galaxyproject.org To subscribe or unsubscribe via the World Wide Web, visit https://lists.galaxyproject.org/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-requ...@lists.galaxyproject.org You can reach the person managing the list at galaxy-dev-ow...@lists.galaxyproject.org When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..." HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. Re: any introduce for how Mako and JavaScript work ingalaxy? (Daniel Blankenberg) 2. Re: ustacks - bad interpreter (Björn Grüning) 3. Re: Improved DRMAAJobRunner (Peter van Heusden) (Matthias Bernt) 4. Re: Improved DRMAAJobRunner (Peter van Heusden) (Peter van Heusden) -- Message: 1 Date: Thu, 6 Jul 2017 22:36:27 -0400 From: Daniel Blankenberg <dan.blankenb...@gmail.com> To: Steven Shen <ishenwei...@gmail.com> Cc: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] any introduce for how Mako and JavaScript work in galaxy? Message-ID: <CAE9nRFg+Edj2=3+K=6+FZCxj5=hb4togw+lm++e+sd1+j2+...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Steven, For a quick first pass, have you taken a look at https://github.com/ galaxyproject/galaxy/blob/dev/client/README.md? Thanks for using Galaxy, Dan On Thu, Jul 6, 2017 at 10:11 PM, Steven Shen <ishenwei...@gmail.com> wrote: Hi everyone, I want to make some change for my local galaxy web, actually I can edit galaxy_path/static/scripts/bundled/*.js directly. It seems mako templates are used for galaxy, as well as many JavaScript files, but I don't know how they work. So is there any introduce for how mako and JavaScript files working in galaxy? Thank you very much. Steven ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ -- next part -- An HTML attachment was scrubbed... URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20170706/8fbd5cbe/attachment-0001.html> -- Message: 2 Date: Sat, 8 Jul 2017 11:31:31 +0200 From: Björn Grüning <bjoern.gruen...@gmail.com> To: David Meltzer <david.melt...@glasgow.ac.uk>, Nate Coraor <n...@bx.psu.edu> Cc: "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyproject.org> Subject: Re: [galaxy-dev] ustacks - bad interpreter Message-ID: <a5a7d281-6040-f65e-e674-6cb2e9343...@gmail.com> Content-Type: text/plain; charset=utf-8 Hi, please also make sure you have a recent conda version. This 80 character length smalls a lot like an old conda restriction. Cheers, Bjoern Am 07.07.2017 um 18:09 schrieb David Meltzer: Good afternoon, Thank you for that! I will look in to it! Best Regards, David Jacob Meltzer *From: *Nate Coraor <n...@bx.psu.edu> *Date: *Friday, July 7, 2017 at 5:02 PM *To: *David Meltzer <david.melt...@glasgow.ac.uk> *Cc: *Yvan Le Bras <yvan.le-b...@mnhn.fr>, "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyproject.org> *Subject: *Re: [galaxy-dev] ustacks - bad interpreter Hi David, You may want to have a look at the first line of: /home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac718a13db6458b9361ca87c93be9feed656f9938ebcc435642f3a0a3/bin/stacks_summary.py The shell is claiming it is: #!/home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac718a1 When it should be: #!/home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac718a13db6458b9361ca87c93be9feed656f9938ebcc435642f3a0a3/bin/python However, it could be that the line is correct and the output was truncated, or the shell has a length limit
Re: [galaxy-dev] Improved DRMAAJobRunner (Peter van Heusden)
Hi Peter, > Code looks interesting. This is for Univa Grid Engine? In its current state its tailored for the Univa Grid Engine. But the drmaa library code that is based on job_info() and wait() should run on all grid engines. For the command line based code changes might be necessary for the different grid engines. (Currently there is only a small bug, because wait() is currently called twice for finished jobs: in the repeated polling and then in the final check. The second call won't work which causes a fallback to qacct. I will fix this soon.) I guess that the output of qstat and qacct will be different. But I think this can be configured one just needs a way to get the info which grid engine is running. > In terms of the upload jobs, are those not designed to be run as 'local' jobs > and not with the 'real user' setting? Sounds reasonable, but this is not what is happening on my installation of galaxy. Any idea where I could start to find the problem. Best, Matthias ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] Improved DRMAAJobRunner
Dear list, I have implemented a new DRMAA job runner allows to detect runtime and memory violations. This is done by using the drmaa library functions job_info + wait or as fallback the commandline tools qstat + qacct. This has the additional advantage that the runner works also in setups using the external runner scripts to start jobs as real user (the original DRMAAJobRunner can not query these jobs at all). You may have a look here: https://github.com/galaxyproject/galaxy/pull/4275 I have successfully tested the but settings: galaxy user/real user submits the jobs. Also the resubmission in case of memory and time violations seems to work. Would be great to get some comments. One problem that I encountered is that upload jobs do not work in the real user setting (for the original and the new runner): The permissions of the uploaded file in /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/ are not changed. Any idea what needs to be changed to get this running? Best, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] AD Intergration
Hi Jelle, I just (in this very moment) solved the "option error" issue for our galaxy installation. see my comment on the first issue mentioned by john: https://github.com/galaxyproject/galaxy/issues/3178#issuecomment-306538866 Maybe you do not need to compile everything from source (as I needed to). Best, Matthias ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] drmaa resubmission
Dear John, thanks a lot for all the information. I guess I will need some time to dig into this. For drmaa the wait() function of the python library seems to return quite bit of useful information: hasExited, hasCoreDump, hasSignal, and terminateSignal. I guess this would be of help. The problem seems to be that when the external run script is used jobs can not be queried properly (see my other post). But I did not understand this completely. Cheers, Matthias On 15.06.2017 19:05, John Chilton wrote: We've done a lot of work in Galaxy dev on this problem over the last few years - I'm not sure how much concrete progress we have made. Nate started it and I did some work at the end of last year. Just to summarize my most recent work on this - in https://github.com/galaxyproject/galaxy/pull/3291/commits/b78287f1508db2c06f0c309ed8d3747adb4d17fa I added some test cases for the existing job runner resubmission stuff - it was just my sense to understand what was there - hopefully the examples in the form of test cases help you as well.. This includes a little test job_conf.xml file that describes how you can catch job walltime and memory limit hits registered by the job runner and send jobs to different destinations. This requires the job runner knows how to record these problems - which the SLURM job runner does - other job runners like the generic drmaa runner may need to be subclassed to check for these things in general. In https://github.com/galaxyproject/galaxy/pull/3291/commits/7d52b28ab2ab0314cd4fa31108a6750cb9750ef3 I created a little DSL for resubmissions to make what can be expressed in job_conf more powerful. Then I added variables to expressions language such as seconds_since_queued, seconds_running(https://github.com/galaxyproject/galaxy/pull/3291/commits/18eb1c8d0e4c3f7616d44fd177c90943695b7053), and attempt number (https://github.com/galaxyproject/galaxy/pull/3291/commits/7e338d790964f594ae67b33e6a72e1777e774b8c). I also added the ability to resubmit on unknown job runner problems here (https://github.com/galaxyproject/galaxy/pull/3291/commits/0559cff6e94b250ddd98275b119ab51b36491e34). None of this is really documented outside the test cases - it is waiting for someone to come along and find it useful. I think the next thing I'd like to see for job resubmission besides documentation and more job runner support for common runners is described in this issue (https://github.com/galaxyproject/galaxy/issues/3320) - all the existing resubmission logic is based on errors detected from job runners - if the underlying error exhibits itself as a tool failure - we need a way to reason about that and we cannot currently. Hope this helps. -John On Thu, Jun 15, 2017 at 10:37 AM, Matthias Bernt <m.be...@ufz.de> wrote: Dear list, I was thinking about implementing the job resubmission feature for drmaa. I hope that I can simplify the job configuration for our installation (and probably others as well) by escalating through different queues (or ressource limits). Thereby I hope to reduce the number of special cases that I need to take care. I was wondering if there are others - who are also interested in this feature and want to join? I would try to give this project a head start in the next week. - that may have started to work on this feature or just started to think about it and want to share code/experience Best, Matthias ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] drmaa job status
Dear Nate and Curtis, I read a bit in the documentation of the python and underlying C library.. and played a bit around. I can't speak for GridEngine's specific behavior because I haven't used it in a long time, but it's not surprising that jobs "disappear" as soon as they've exited. Unfortunately, Galaxy uses periodic polling rather than waiting on completion. We'd need to create a thread-per-submitted job unless you can still get job exit details by looping over jobs with a timeout wait. > > You can gain some control over how Galaxy handles InvalidJobException exceptions with drmaa job runner plugin params, see here: https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L9 However, if normally finished jobs also result in InvalidJobException, that probably won't help. Alternatively, you could create a DRMAAJobRunner subclass for GridEngine like we've done for Slurm that does some digging to learn more about terminal jobs. I found a way to get the information. The problem in my script was that wait() "reaps" (that the term used by python-drmaa) all information on the job from the session(?). Hence calls to jobStatus after wait() will fail. The solution here would be to use synchronize() with parameter dispose=False, see attached file -- alternatively one can also wait until job status is DONE or FAILED. But this seems not to be the source of the problem within Galaxy, since it never calls wait(..). The problem seems to be that an external python script submits the job in another session (when jobs are submitted as real user). The problem is then that jobs created in another session can not be queried (The documentation is a bit vague here: in the C library documentation of SGE I read that it is definitely not possible to query finished jobs). I tried if it is possible to pickle the session -- without success. Does anyone has an idea how one could get the active drmaa session from galaxy to the external script? > We have had this problem on our SGE based installation for years. We > referred to it as the "green screen of death" - as it would allow a > biologist to continue analysis using output that was partial, at best, > often resulting in seemingly successful completion of the entire > analysis, but completely bogus results (say, cuffdiff killed half way > through the genome, but it's green in galaxy, so no transcripts on the > smaller chromosomes, but no error, either). Did you use submission as real user? Or does the problem also appear if jobs are submitted as the single user running galaxy. > We ended up implementing an external reaper that detected these killed > jobs from SGE, and notified the user and galaxy post-hoc. It was not a > very satisfactory solution. We are currently moving to SLURM for other > reasons and hope the problem will not be present there. I was also thinking about not using the python library at all, but using system calls to qsub, qkill, qacct, etc? Any opinions on this idea? I guess your reaper could be of interest also for others. Is this available somewhere? Best, Matthias --nate On Thu, Jun 15, 2017 at 10:27 AM, Matthias Bernt <m.be...@ufz.de <mailto:m.be...@ufz.de>> wrote: Dear list, I have two question for all DRMAA users. Here is the first one. I was checking how our queuing system (univa GridEngine) and Galaxy react if jobs are submitted that exceed run time or memory limits. I found out that the python drmaa library cannot query the job status after the job is finished (for both successful and unsuccessful jobs). In lib/galaxy/jobs/runners/drmaa.py the call gives an exception self.ds.job_status( external_job_id ) Is this always the case? Or might this be a problem with our GridEngine? I have attached some code for testing. Here the first call to s.jobStatus(jobid) works, but the second after s.wait(...) doesn't. But I get "drmaa.errors.InvalidJobException: code 18: The job specified by the 'jobid' does not exist." The same error pops up in the Galaxy logs. The consequence is that jobs that reached the limits are shown as completed successfully in Galaxy. Interestingly, quite a bit of information can be obtained from the return value of s.wait. I was wondering if this can be used to differentiate successful from failed jobs. In particular hasExited, hasSignal, and terminateSignal are different in the two cases. Cheers, Matthias ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/> To search Galaxy mai
[galaxy-dev] drmaa resubmission
Dear list, I was thinking about implementing the job resubmission feature for drmaa. I hope that I can simplify the job configuration for our installation (and probably others as well) by escalating through different queues (or ressource limits). Thereby I hope to reduce the number of special cases that I need to take care. I was wondering if there are others - who are also interested in this feature and want to join? I would try to give this project a head start in the next week. - that may have started to work on this feature or just started to think about it and want to share code/experience Best, Matthias ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] drmaa job status
Dear list,
I have two question for all DRMAA users. Here is the first one.
I was checking how our queuing system (univa GridEngine) and Galaxy
react if jobs are submitted that exceed run time or memory limits.
I found out that the python drmaa library cannot query the job status
after the job is finished (for both successful and unsuccessful jobs).
In lib/galaxy/jobs/runners/drmaa.py the call gives an exception
self.ds.job_status( external_job_id )
Is this always the case? Or might this be a problem with our GridEngine?
I have attached some code for testing. Here the first call to
s.jobStatus(jobid) works, but the second after s.wait(...) doesn't.
But I get "drmaa.errors.InvalidJobException: code 18: The job specified
by the 'jobid' does not exist."
The same error pops up in the Galaxy logs. The consequence is that jobs
that reached the limits are shown as completed successfully in Galaxy.
Interestingly, quite a bit of information can be obtained from the
return value of s.wait. I was wondering if this can be used to
differentiate successful from failed jobs. In particular hasExited,
hasSignal, and terminateSignal are different in the two cases.
Cheers,
Matthias
#!/usr/bin/env python
from __future__ import print_function
import drmaa
import os
def main():
"""Submit a job.
Note, need file called sleeper.sh in current directory.
"""
with drmaa.Session() as s:
print('Creating job template')
jt = s.createJobTemplate()
jt.jobName = "foo"
jt.workingDirectory = "/home/songalax/"
jt.remoteCommand = '/home/songalax/sleeper.sh'
jt.args = ['30','Simon_says']
jt.joinFiles=True
jt.nativeSpecification = "-l h_rt=10 -l h_vmem=1G -pe smp 2 -w n"
#
jobid = s.runJob(jt)
print('Your job has been submitted with id ' + jobid)
decodestatus = {drmaa.JobState.UNDETERMINED: 'process status cannot be determined',
drmaa.JobState.QUEUED_ACTIVE: 'job is queued and active',
drmaa.JobState.SYSTEM_ON_HOLD: 'job is queued and in system hold',
drmaa.JobState.USER_ON_HOLD: 'job is queued and in user hold',
drmaa.JobState.USER_SYSTEM_ON_HOLD: 'job is queued and in user and system hold',
drmaa.JobState.RUNNING: 'job is running',
drmaa.JobState.SYSTEM_SUSPENDED: 'job is system suspended',
drmaa.JobState.USER_SUSPENDED: 'job is user suspended',
drmaa.JobState.DONE: 'job finished normally',
drmaa.JobState.FAILED: 'job finished, but failed'}
print(decodestatus[s.jobStatus(jobid)])
retval = s.wait(jobid, drmaa.Session.TIMEOUT_WAIT_FOREVER)
print('Job: {0} finished with status {1}'.format(retval.jobId, retval.hasExited))
print("exitStatus {0}\nhasCoreDump {1}\nhasExited {2}\nhasSignal {3}\njobId {4}\nresourceUsage {5}\nterminatedSignal {6}wasAborted {7}\n".format(retval.exitStatus, retval.hasCoreDump, retval.hasExited, retval.hasSignal, retval.jobId, retval.resourceUsage, retval.terminatedSignal, retval.wasAborted))
print(decodestatus[s.jobStatus(jobid)])
print('Cleaning up')
s.deleteJobTemplate(jt)
if __name__=='__main__':
main()
sleeper.sh
Description: application/shellscript
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[galaxy-dev] protein ligand docking
Dear list, I have recently evaluated the software for protein docking that is available in the toolshed. I could need some help / suggestions. 1. autodock_vina The receptor of my example contains Au atoms which are not understood by autodock_vina. For autodock there is the possibility to add configuration for atoms: http://autodock.scripps.edu/faqs-help/how-to/adding-new-atom-parameters-to-autodock Does somebody know if this is also possible for autodock_vina in galaxy? In my pdb file there are CONECT lines which cause autodock_vina to abort. If I remove them the program runs (when the Au atoms are also removed). So this is the smaller problem (Maybe this can be solved by extending openbabel). 2. rdock Fails with a memory access failure /gpfs1/data/galaxy_server/galaxy-dev/database/dependencies/_conda/envs/__rDock@2013.1/bin/rbcavity: Zeile 7: 104454 Speicherzugriffsfehler (Speicherabzug geschrieben) "$RBT_ROOT/bin/$PROGNAME" "$@" 3. caddsuite_workflows + caddsuite_linux_x86_64 The installation of the workflows works, but I do not see them in galaxy? The installation of the other package fails with: No information is available for the requested repository revision. One or more of the following parameter values is likely invalid: tool_shed_url: https://toolshed.g2.bx.psu.edu/ name: caddsuite_linux_x86_64 owner: marcel changeset_revision: 026f5a483650 err_code: 48 4. BALL I just tested one tool of the suite: ProteinProtonator. This fails with command not found. Fatal error: Exit code 127 () /gpfs1/data/galaxy_server/galaxy-dev/jobs_dir/000/165/tool_script.sh: Zeile 9: ProteinProtonator: Kommando nicht gefunden. Are there any suggestion on how to solve these problems or other options for docking with galaxy. Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- smime.p7s Description: S/MIME Cryptographic Signature ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] cluster access
Dear list, I had some time to dig into this. Since this is a quite old thread here is a wrap up: The problem was that galaxy uses the USER part of the email address (USER@DOMAIN) to determine the system user to submit jobs to a drmaa cluster (I need to submit jobs as real user). In my setting, where users login via LDAP, this does not work since the prefix of the email is not always the user name, but the actual user is stored in the galaxy data base (and awaited utilization :) ). I found a way to let galaxy try both possibilities, and whatever of the two possibilities matches a real user is taken (prioritizing the email method for compatibility). I have created a pull request: https://github.com/galaxyproject/galaxy/pull/4096 Cheers, Matthias On 10.04.2017 17:03, Peter Cock wrote: That's interesting. I didn't set this up on our system, but if the LDAP can tell Galaxy the real username, maybe we can avoid having to setup usern...@example.org aliases and insisting our users do that for logging into Galaxy. Hopefully some other SGE users can comment on how they got the run-as-user system working for them? Peter On Mon, Apr 10, 2017 at 3:43 PM, Matthias Bernt <m.be...@ufz.de> wrote: Hi, sorry, I forgot this central piece of information: We also use Univa Grid Engine. What would be easier adapting galaxy's mapping to users or setting up email aliases? I would need to ask our cluster admins if they could realize this. Best, Matthias On 10.04.2017 16:39, Peter Cock wrote: This may depend on the cluster setup, and how Galaxy accesses it. What are you using? We use SGE (actually Univa Grid Engine) via DRMAA, and had to setup usern...@example.org email aliases just for this. Peter On Mon, Apr 10, 2017 at 3:36 PM, Matthias Bernt <m.be...@ufz.de> wrote: Dear list, I'm just starting to get jobs submitted to our cluster as real system user. I read in the documentation that the name of the system user is determined by "the Galaxy user's email address (with the @domain stripped off)". But this does not work on our system, rather the username stored in the galaxy_user table is the name of the user (this is correctly generated by the LDAP login). The job runner script seems to get the user id, so I guess I need to dig deeper. So my question is: Where could I change this behavior? Thanks a lot. Cheers, Matthias -- ------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Mana
Re: [galaxy-dev] OpenBabel Requirements
Hi Bjoern, I thought I'm using conda .. :). I'm using the ansible galaxy-tools-playbook to install tools. I tried before if ansible installation and installation via the web interface give the same results -- and I recalled that the results were identical. But I was wrong -- sorry for the inconvenience. Now, when installing via ansible I'm getting identical (compared to installation via the web interface) results for blat I choose the following options in the tool_list.yaml file. install_tool_dependencies: False install_repository_dependencies: True install_resolver_dependencies: True But I still have not understood the dependencies (and dependency problems) shown in the web interface... Maybe you could explain this to me? In the logs there is first a complaint about missing - blat 35x1* then the following packages are installed: blat: 35-1 bioconda libpng: 1.6.27-0 zlib: 1.2.8-3 The admin interface puzzles me: For the blat package: - "Dependency Resolver Details" lists blat 35x1 as resolved but not the exact version. This seems to be fine. - Installed repository dependencies lists package_blat_35x1 as installed but missing dependencies. This is odd? Why is this installed at all? For the package_blat_35x1 - Installed repository dependencies lists package_libpng_1_6_7 - Missing tool dependencies lists blat and libpng. The circular dependency to blat is strange, isn't it? Thanks again for the support. Cheers, Matthias On 18.05.2017 17:09, Björn Grüning wrote: Hi Matthias, is there any chance you can upgrade your Galaxy and enable conda packages? This would make your life so much easier :) Cheers, Bjoern Am 18.05.2017 um 16:28 schrieb Matthias Bernt: Hi Bjoern, thanks for the explanation. This helped for the openbabel package. Still there are some packages where I have problems. I guess this is because on our system the libraries are mostly at non-default locations. Currently I have problems to install BLAT. It complains about a missing zlib. Zlib is installed and the path to the includes is in CPPFLAGS. Is there any variable that would make it known to the installation process? gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOU RCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I/gpfs1/data/galaxy_server/gala xy-dev/database/dependencies/libpng/1.6.7/devteam/package_libpng_1_6_7/3de32cd300a9/include -o zlibFace.o -c zlibFace.c make: Leaving directory `/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtd4Jyr2N/blat/src /lib' zlibFace.c:4:18: error: zlib.h: No such file or directory An additional question for understanding: There are packages for zlib and cmake (as example). Why are these not used? Is this because there is still transition to conda -- which will just need time? But from an earlier post I thought I understood that package_* is the old non-conda way. Or is the intended future state that central packages mentioned in https://galaxyproject.org/toolshed/package-recipes/ are managed on the system .. and not conda? Thanks a lot. Cheers, Matthias On 17.05.2017 20:08, Björn Grüning wrote: Hi Matthias, if you are installing repositories that still rely on the old traditional Galaxy system you need to have a few packages installed locally, see this list: https://galaxyproject.org/toolshed/package-recipes/ However, we have now a new dependency system in Galaxy, that is build on-top of conda and most of the Cheminformatic tools have been ported to Conda already. Which version of Galaxy are you running? But maybe I have also not pushed the latest changes to the toolshed which I have been working on github :( Ciao, Bjoern Am 17.05.2017 um 17:04 schrieb Matthias Bernt: Dear galaxy-dev list, I have problems to install package_openbabel. The problem seems to be that cmake is not found during installation. The documentation also states that: "Compiling OpenBabel requires g++ and CMake 2.4+" My question is: Does this refer to cmake installed on the system or in galaxy (since there is also package_cmake_3_2_3)? Thanks a lot. Cheers, Matthias ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ -- ------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be..
Re: [galaxy-dev] OpenBabel Requirements
Hi Bjoern, thanks for the explanation. This helped for the openbabel package. Still there are some packages where I have problems. I guess this is because on our system the libraries are mostly at non-default locations. Currently I have problems to install BLAT. It complains about a missing zlib. Zlib is installed and the path to the includes is in CPPFLAGS. Is there any variable that would make it known to the installation process? gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOU RCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I/gpfs1/data/galaxy_server/gala xy-dev/database/dependencies/libpng/1.6.7/devteam/package_libpng_1_6_7/3de32cd300a9/include -o zlibFace.o -c zlibFace.c make: Leaving directory `/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtd4Jyr2N/blat/src /lib' zlibFace.c:4:18: error: zlib.h: No such file or directory An additional question for understanding: There are packages for zlib and cmake (as example). Why are these not used? Is this because there is still transition to conda -- which will just need time? But from an earlier post I thought I understood that package_* is the old non-conda way. Or is the intended future state that central packages mentioned in https://galaxyproject.org/toolshed/package-recipes/ are managed on the system .. and not conda? Thanks a lot. Cheers, Matthias On 17.05.2017 20:08, Björn Grüning wrote: Hi Matthias, if you are installing repositories that still rely on the old traditional Galaxy system you need to have a few packages installed locally, see this list: https://galaxyproject.org/toolshed/package-recipes/ However, we have now a new dependency system in Galaxy, that is build on-top of conda and most of the Cheminformatic tools have been ported to Conda already. Which version of Galaxy are you running? But maybe I have also not pushed the latest changes to the toolshed which I have been working on github :( Ciao, Bjoern Am 17.05.2017 um 17:04 schrieb Matthias Bernt: Dear galaxy-dev list, I have problems to install package_openbabel. The problem seems to be that cmake is not found during installation. The documentation also states that: "Compiling OpenBabel requires g++ and CMake 2.4+" My question is: Does this refer to cmake installed on the system or in galaxy (since there is also package_cmake_3_2_3)? Thanks a lot. Cheers, Matthias ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- smime.p7s Description: S/MIME Cryptographic Signature ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] OpenBabel Requirements
Dear galaxy-dev list, I have problems to install package_openbabel. The problem seems to be that cmake is not found during installation. The documentation also states that: "Compiling OpenBabel requires g++ and CMake 2.4+" My question is: Does this refer to cmake installed on the system or in galaxy (since there is also package_cmake_3_2_3)? Thanks a lot. Cheers, Matthias smime.p7s Description: S/MIME Cryptographic Signature ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] conda installation fails
Dear list, found a solution (aka dirty hack), if anybody is interested: The problem is that our cluster uses environment modules (http://modules.sourceforge.net/) to provide software (basically by setting and unsetting PATHs...). Because python needs bz2 support for galaxy I needed to load bzip2 as module since the dynamic library was not available otherwise. This module also provides a bunzip2 binary which led to a clash when the LD_LIBRARY_PATH was unset during conda installation (the module's bunzip2 still wanted to have the dynamic library and the systems bunzip2 was later in the PATH). Solution: I created a copy of the module which appends the needed paths to the various environment variables (instead of prepending). Then the systems bunzip2 used and the shared object is still available. Cheers, Matthias On 19.04.2017 18:15, Marius van den Beek wrote: That's a little weird, I don't think relying on the system's LD_LIBRARY_PATH is good practice. Maybe you could try what was suggested in the last answer here: https://serverfault.com/questions/372987/centos-usr-local-lib-system-wide-ld-library-path. On 19 April 2017 at 17:57, Matthias Bernt <m.be...@ufz.de <mailto:m.be...@ufz.de>> wrote: Dear list, Just found out that conda is not installing on our CentOS6.8 installation (might be related to earlier messages). The problem is that the shell script installing conda unsets the LD_LIBRARY_PATH which makes tar dysfunctional (tar is called by the installer). The command line that is executed during galaxy's installation is wget -q --recursive -O '/tmp/conda_install7tWo7r.sh' 'https://repo.continuum.io/miniconda/Miniconda3-4.2.12-Linux-x86_64.sh <https://repo.continuum.io/miniconda/Miniconda3-4.2.12-Linux-x86_64.sh>' && bash '/tmp/conda_install7tWo7r.sh' -b -p '/gpfs1/data/galaxy_server/galaxy-dev/_conda' && /gpfs1/data/galaxy_server/galaxy-dev/_conda/bin/conda install -y -q conda=4.2.13 Removing the unset LD_LIBRARY_PATH line (and fiddling around with some file size checks) is (seemingly) successful. There is an open issue on the conda github: https://github.com/conda/conda/issues/3632 <https://github.com/conda/conda/issues/3632> Any suggestions? The line removal procedure seems to be quite complicated in an automated ansible installation which I try to achieve. Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296 <tel:%2B49%20341%20235%20482296>, m.be...@ufz.de <mailto:m.be...@ufz.de>, www.ufz.de <http://www.ufz.de> Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/> To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/search/> -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- smime.p7s Description: S/MIME Cryptographic Signature ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and othe
[galaxy-dev] conda installation fails
Dear list, Just found out that conda is not installing on our CentOS6.8 installation (might be related to earlier messages). The problem is that the shell script installing conda unsets the LD_LIBRARY_PATH which makes tar dysfunctional (tar is called by the installer). The command line that is executed during galaxy's installation is wget -q --recursive -O '/tmp/conda_install7tWo7r.sh' 'https://repo.continuum.io/miniconda/Miniconda3-4.2.12-Linux-x86_64.sh' && bash '/tmp/conda_install7tWo7r.sh' -b -p '/gpfs1/data/galaxy_server/galaxy-dev/_conda' && /gpfs1/data/galaxy_server/galaxy-dev/_conda/bin/conda install -y -q conda=4.2.13 Removing the unset LD_LIBRARY_PATH line (and fiddling around with some file size checks) is (seemingly) successful. There is an open issue on the conda github: https://github.com/conda/conda/issues/3632 Any suggestions? The line removal procedure seems to be quite complicated in an automated ansible installation which I try to achieve. Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- smime.p7s Description: S/MIME Cryptographic Signature ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] atlas version 3.10.2 installation error
Dear Peter, thanks. Just for understanding: Why not just change the biopython dependency from 1.67 to 1.69, if this is the one available in bioconda. blast_rbh seems to use only the SeqIO fasta parser and writer. This should be no problem. But I guess that for older versions of blast_rbh one might still need legacy packages of biopython. Or could one change the dependencies in older versions? Or would this be no good idea because of backward compatibility? Cheers, Matthias On 19.04.2017 13:50, Peter Cock wrote: Just lucky timing, could you try blast_rbh v0.1.11, https://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh/d8d9a9069586 For BLAST+ this ought to work with either bioconda, or the legacy XML based packages, as both have BLAST+ 2.5.0. However, it looks like bioconda only has Biopython 1.68 and 1.69, while the legacy XML based packages only go up to Biopython 1.67 at the time of writing... it looks like we'll need to add a couple more legacy packages. Peter On Wed, Apr 19, 2017 at 12:01 PM, Matthias Bernt <m.be...@ufz.de> wrote: Dear Peter, thanks for the info. Would be great to get the update, but since I have a method that is working for the moment there is no need to hurry. Best, Matthias On 19.04.2017 12:57, Peter Cock wrote: Oh right - I've just been updating ncbi_blast_plus this morning to transition to BLAST+ 2.5.0 via either bioconda or the older legacy Tool Shed. I can try to update blast_rbh next, which may solve this by letting you use bioconda. Peter On Wed, Apr 19, 2017 at 11:52 AM, Matthias Bernt <m.be...@ufz.de> wrote: Dear Marius, thanks again for the help. I'm trying to install blast_rbh (owner is peterjc). The dependencies look as follows: blast_rbh - biopython - package_biopython_1_64 - package_numpy_1_8 - package_atlas_3_10 - blast - package_blast_plus_2_2_31 - blast+ With unchecked "When available, install Tool Shed managed tool dependencies?" I get all as "Installed, missing tool dependencies". Blast_rbh is not working since blast+ is not installed. Even if I install blast+ manually (in galaxy) its not working (makeblastdb is missing). When I leave "When available, install Tool Shed managed tool dependencies?" I see blast_rbh, package_blast_plus package_biopython as installed and the others as Installed, missing tool dependencies. Here blast_rbh is working. What would be your suggestion? Live with the latter and file an issue at the tools repository (difficult to say which causes the problem(s))? I get similar behavior if I try to install from the test toolshed. (Only a different error from atlas: /bin/sh: line 3: /host/static_full_blas_lapack.diff: No such file or directory). But, actually I'm trying to automatize tool installation using the ansible role ansible-galaxy-tools (https://github.com/galaxyproject/ansible-galaxy-tools). With this method I get the latter behavior. The role uses uses ephemeris==0.4.0 to install tools. There I have seen three global variables that (I guess) control the installation of dependencies. INSTALL_TOOL_DEPENDENCIES = False INSTALL_REPOSITORY_DEPENDENCIES = True INSTALL_RESOLVER_DEPENDENCIES = True I guess I could control the behavior with the latter two variables. Best, Matthias On 18.04.2017 19:24, Marius van den Beek wrote: Hi Matthias, it's me again! What tool are you trying to install? My -perhaps- unhelpful suggestion is to not install anything that starts with package_* (also called tool shed packages), those should be exclusively installed when you absolutely need to install an old tool that can only function with packages. We've switched to conda nowadays, which is much easier to install and to maintain. In fact the IUC has ported all their latest tools to conda, and similarly most devteam tools that are still in active use have also been ported to use Conda dependencies. If you look at this document https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/, there is a part where you confirm dependencies. If you click on show detail, and you unselect When available, install Tool Shed managed tool dependencies? Galaxy will not try to install these old packages. There are some tools which come both with old toolshed dependencies and that have Conda available. You may be lucky and find that the tool you are trying to install has Conda dependencies available. There is a lot more background on the Toolshed and Conda in this document here: https://docs.galaxyproject.org/en/master/admin/conda_faq.html Best, Marius On 18 April 2017 at 19:03, Matthias Bernt <m.be...@ufz.de <mailto:m.be...@ufz.de>> wrote: Dear list, again me :( stumbling from problem to problem ... I got compilation errors when installing package_atlas_3_10 Revision: 98c017ec230d I tried with gcc 4x and 6x without success. Do I need the intel C compiler for this tool? If I got earlier posts (http://dev
Re: [galaxy-dev] atlas version 3.10.2 installation error
Dear Peter, thanks for the info. Would be great to get the update, but since I have a method that is working for the moment there is no need to hurry. Best, Matthias On 19.04.2017 12:57, Peter Cock wrote: Oh right - I've just been updating ncbi_blast_plus this morning to transition to BLAST+ 2.5.0 via either bioconda or the older legacy Tool Shed. I can try to update blast_rbh next, which may solve this by letting you use bioconda. Peter On Wed, Apr 19, 2017 at 11:52 AM, Matthias Bernt <m.be...@ufz.de> wrote: Dear Marius, thanks again for the help. I'm trying to install blast_rbh (owner is peterjc). The dependencies look as follows: blast_rbh - biopython - package_biopython_1_64 - package_numpy_1_8 - package_atlas_3_10 - blast - package_blast_plus_2_2_31 - blast+ With unchecked "When available, install Tool Shed managed tool dependencies?" I get all as "Installed, missing tool dependencies". Blast_rbh is not working since blast+ is not installed. Even if I install blast+ manually (in galaxy) its not working (makeblastdb is missing). When I leave "When available, install Tool Shed managed tool dependencies?" I see blast_rbh, package_blast_plus package_biopython as installed and the others as Installed, missing tool dependencies. Here blast_rbh is working. What would be your suggestion? Live with the latter and file an issue at the tools repository (difficult to say which causes the problem(s))? I get similar behavior if I try to install from the test toolshed. (Only a different error from atlas: /bin/sh: line 3: /host/static_full_blas_lapack.diff: No such file or directory). But, actually I'm trying to automatize tool installation using the ansible role ansible-galaxy-tools (https://github.com/galaxyproject/ansible-galaxy-tools). With this method I get the latter behavior. The role uses uses ephemeris==0.4.0 to install tools. There I have seen three global variables that (I guess) control the installation of dependencies. INSTALL_TOOL_DEPENDENCIES = False INSTALL_REPOSITORY_DEPENDENCIES = True INSTALL_RESOLVER_DEPENDENCIES = True I guess I could control the behavior with the latter two variables. Best, Matthias On 18.04.2017 19:24, Marius van den Beek wrote: Hi Matthias, it's me again! What tool are you trying to install? My -perhaps- unhelpful suggestion is to not install anything that starts with package_* (also called tool shed packages), those should be exclusively installed when you absolutely need to install an old tool that can only function with packages. We've switched to conda nowadays, which is much easier to install and to maintain. In fact the IUC has ported all their latest tools to conda, and similarly most devteam tools that are still in active use have also been ported to use Conda dependencies. If you look at this document https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/, there is a part where you confirm dependencies. If you click on show detail, and you unselect When available, install Tool Shed managed tool dependencies? Galaxy will not try to install these old packages. There are some tools which come both with old toolshed dependencies and that have Conda available. You may be lucky and find that the tool you are trying to install has Conda dependencies available. There is a lot more background on the Toolshed and Conda in this document here: https://docs.galaxyproject.org/en/master/admin/conda_faq.html Best, Marius On 18 April 2017 at 19:03, Matthias Bernt <m.be...@ufz.de <mailto:m.be...@ufz.de>> wrote: Dear list, again me :( stumbling from problem to problem ... I got compilation errors when installing package_atlas_3_10 Revision: 98c017ec230d I tried with gcc 4x and 6x without success. Do I need the intel C compiler for this tool? If I got earlier posts (http://dev.list.galaxyproject.org/atlas-3-10-IUC-error-tt4668236.html <http://dev.list.galaxyproject.org/atlas-3-10-IUC-error-tt4668236.html>) correct a precompiled version should be used anyway? I'm running galaxy on CentOS 6.8 (64bit) (running in a VirtualBox). Best, Matthias Here is the output (which I guess is verbose output from configure): /tmp/cctyMGAH.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' probe_OS.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' probe_asm.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkste
Re: [galaxy-dev] atlas version 3.10.2 installation error
Dear Marius, thanks again for the help. I'm trying to install blast_rbh (owner is peterjc). The dependencies look as follows: blast_rbh - biopython - package_biopython_1_64 - package_numpy_1_8 - package_atlas_3_10 - blast - package_blast_plus_2_2_31 - blast+ With unchecked "When available, install Tool Shed managed tool dependencies?" I get all as "Installed, missing tool dependencies". Blast_rbh is not working since blast+ is not installed. Even if I install blast+ manually (in galaxy) its not working (makeblastdb is missing). When I leave "When available, install Tool Shed managed tool dependencies?" I see blast_rbh, package_blast_plus package_biopython as installed and the others as Installed, missing tool dependencies. Here blast_rbh is working. What would be your suggestion? Live with the latter and file an issue at the tools repository (difficult to say which causes the problem(s))? I get similar behavior if I try to install from the test toolshed. (Only a different error from atlas: /bin/sh: line 3: /host/static_full_blas_lapack.diff: No such file or directory). But, actually I'm trying to automatize tool installation using the ansible role ansible-galaxy-tools (https://github.com/galaxyproject/ansible-galaxy-tools). With this method I get the latter behavior. The role uses uses ephemeris==0.4.0 to install tools. There I have seen three global variables that (I guess) control the installation of dependencies. INSTALL_TOOL_DEPENDENCIES = False INSTALL_REPOSITORY_DEPENDENCIES = True INSTALL_RESOLVER_DEPENDENCIES = True I guess I could control the behavior with the latter two variables. Best, Matthias On 18.04.2017 19:24, Marius van den Beek wrote: Hi Matthias, it's me again! What tool are you trying to install? My -perhaps- unhelpful suggestion is to not install anything that starts with package_* (also called tool shed packages), those should be exclusively installed when you absolutely need to install an old tool that can only function with packages. We've switched to conda nowadays, which is much easier to install and to maintain. In fact the IUC has ported all their latest tools to conda, and similarly most devteam tools that are still in active use have also been ported to use Conda dependencies. If you look at this document https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/, there is a part where you confirm dependencies. If you click on show detail, and you unselect When available, install Tool Shed managed tool dependencies? Galaxy will not try to install these old packages. There are some tools which come both with old toolshed dependencies and that have Conda available. You may be lucky and find that the tool you are trying to install has Conda dependencies available. There is a lot more background on the Toolshed and Conda in this document here: https://docs.galaxyproject.org/en/master/admin/conda_faq.html Best, Marius On 18 April 2017 at 19:03, Matthias Bernt <m.be...@ufz.de <mailto:m.be...@ufz.de>> wrote: Dear list, again me :( stumbling from problem to problem ... I got compilation errors when installing package_atlas_3_10 Revision: 98c017ec230d I tried with gcc 4x and 6x without success. Do I need the intel C compiler for this tool? If I got earlier posts (http://dev.list.galaxyproject.org/atlas-3-10-IUC-error-tt4668236.html <http://dev.list.galaxyproject.org/atlas-3-10-IUC-error-tt4668236.html>) correct a precompiled version should be used anyway? I'm running galaxy on CentOS 6.8 (64bit) (running in a VirtualBox). Best, Matthias Here is the output (which I guess is verbose output from configure): /tmp/cctyMGAH.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' probe_OS.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' probe_asm.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' system(make IRun_GAS_x8632 args="-v 2" MYFLAGS="-DATL_OS_Linux" 2> /dev/null | fgrep SUCCESS) ierr=256 in command='make IRun_GAS_x8632 args="-v 2" MYFLAGS="-DATL_OS_Linux" 2> /dev/null | fgrep SUCCESS'! OUTPUT: === system(make IRun_GAS_x8664 args="-v 2" MYFLAGS="-DATL_OS_Linux" 2> /dev/null | fgrep SUCCESS) probe_vec.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-de
[galaxy-dev] atlas version 3.10.2 installation error
='gcc' '-O2 -fomit-frame-pointer -mfpmath=sse -fno-schedule-insns -fno-optimize-register-move' 76. priority=1000, comps,OS,arch[0]=(25,1,-2147483648), comp='gcc' '-O2 -fomit-frame-pointer -mfpmath=sse' 77. priority=1000, comps,OS,arch[0]=(128,1,-1073741824), comp='gfortran' '-O2 -fomit-frame-pointer -mfpmath=sse' 78. priority=1000, comps,OS,arch[0]=(128,1,32768), comp='gfortran' '-fomit-frame-pointer -mfpmath=sse -O2' 79. priority=1000, comps,OS,arch[0]=(95,1,32768), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 80. priority=1000, comps,OS,arch[0]=(128,1,16384), comp='gfortran' '-fomit-frame-pointer -mfpmath=sse -O2' 81. priority=1000, comps,OS,arch[0]=(95,1,16384), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 82. priority=1000, comps,OS,arch[0]=(128,1,8192), comp='gfortran' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 83. priority=1000, comps,OS,arch[0]=(10,1,8192), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 84. priority=1000, comps,OS,arch[0]=(85,1,8192), comp='gcc' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 85. priority=1000, comps,OS,arch[0]=(128,1,12288), comp='gfortran' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 86. priority=1000, comps,OS,arch[0]=(95,1,4096), comp='gcc' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 87. priority=1000, comps,OS,arch[0]=(65,1,536870912), comp='gcc' '-O' 88. priority=1000, comps,OS,arch[0]=(30,1,536870912), comp='gcc' '-O3 -fno-schedule-insns2 -funroll-all-loops -fno-tree-ch' 89. priority=1000, comps,OS,arch[0]=(95,1,33554432), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 90. priority=1005, comps,OS,arch[0]=(31,896,33554432), comp='gcc-4' '-fomit-frame-pointer -mfpmath=sse -O2' 91. priority=1000, comps,OS,arch[0]=(95,1,67108864), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2' 92. priority=1005, comps,OS,arch[0]=(95,896,67108864), comp='gcc-4' '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2' 93. priority=50, comps,OS,arch[0]=(57,1,134217728), comp='clang' '-fomit-frame-pointer -mavx -O2 -m64 -Wno-parentheses' 94. priority=1000, comps,OS,arch[0]=(127,1,134217728), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2' 95. priority=1005, comps,OS,arch[0]=(31,896,134217728), comp='gcc-4' '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2' 96. priority=1000, comps,OS,arch[0]=(127,1,268435456), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' Compiler nodes: Targeted 0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77' '-O' 1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77' '-O' 2. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran' '-O' 3. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc' '-O -fomit-frame-pointer' Compiler nodes: Sorted 0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77' '-O' 1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77' '-O' 2. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc' '-O -fomit-frame-pointer' 3. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran' '-O' cc1: error: unrecognized command line option "-mavx2" make[2]: *** [IRunCComp] Error 1 ierr=256 in command='make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O -fomit-frame-pointer -mavx2 -mfma -fPIC -m64' | fgrep SUCCESS'! OUTPUT: === cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O -fomit-frame-pointer -mavx2 -mfma -fPIC -m64' | fgrep SUCCESS /usr/bin/gcc -O -fomit-frame-pointer -mavx2 -mfma -fPIC -m64 : FAILURE! Unable to find usable compiler for ICC; abortingMake sure compilers are in your path, and specify good compilers to configure (see INSTALL.txt or 'configure --help' for details)make[1]: *** [atlas_run] Error 1 make: *** [IRun_comp] Error 2 ERROR 512 IN SYSCMND: 'make IRun_comp args="-v 2 -o atlconf.txt -O 1 -A 39 -Si nof77 0 -V 488 -Fa ic '-fPIC' -Fa sm '-fPIC' -Fa dm '-fPIC' -Fa sk '-fPIC' -Fa dk '-fPIC' -Fa xc '-fPIC' -Fa gc '-fPIC' -Fa if '-fPIC' -b 64"' Make.top:1: Make.inc: No such file or directory Make.top:329: warning: overriding commands for target `/AtlasTest' Make.top:80: warning: ignoring old commands for target `/AtlasTest' make[1]: *** No rule to make target `Make.inc'. Stop. make: *** [startup] Error 2 mv: cannot stat `lib/Makefile': No such file or directory ../configure: line 450: lib/Makefile: No such file or directory ../configure: line 451: lib/Makefile: No such file or directory ../configure: line 452: lib/Makefile: No such file or directory ../configure: line 453: lib/Makefile: No such file or directory ../configure: line 509: lib/Makefile: No such file or directory Make.top:1: Make.inc: No such file or directory Make.top:329: warning: overriding commands for target `/AtlasTest' Make.top:80: warning: ignoring old commands for target `/AtlasTest' make[1]: *** No rule to make
Re: [galaxy-dev] SSL certificate errors
Hi Marius, thanks a lot -- you made my day! The solution was: export SSL_CERT_FILE=/etc/pki/tls/certs/ca-bundle.crt Cheers, Matthias On 18.04.2017 17:39, Marius van den Beek wrote: Hi Matthias, this looks like your python installation does not know how to verify SSL certificates. Redhat have a nice section on troubleshooting that here: https://access.redhat.com/articles/2039753 I can get your error by specifying a nonexsting cert: |mvandenb@Mariuss-MacBook-Pro:~/src/readtagger/readtagger (master)*$ SSL_CERT_FILE=/does_not_exist python ~/urllib2_test.py https://usegalaxy.org Traceback (most recent call last): File "/Users/mvandenb/urllib2_test.py", line 10, in urllib2.urlopen(req) File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 154, in urlopen return opener.open(url, data, timeout) File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 429, in open response = self._open(req, data) File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 447, in _open '_open', req) File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 407, in _call_chain result = func(*args) File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 1241, in https_open context=self._context) File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 1198, in do_open raise URLError(err) urllib2.URLError: | Hope that helps, Marius On 18 April 2017 at 17:13, Matthias Bernt <m.be...@ufz.de <mailto:m.be...@ufz.de>> wrote: Dear list, Currently I get SSL certificate errors when I try to install a tool in Galaxy. I also get the same error when I try to use the galaxy-tools ansible role (when debugging this I thought this might be because my local server is on http, since the error appeared seemingly when a message was posted to the local server -- but I'm not entirely sure). I'm also missing the "Manage installed tools" link in the admin area (but maybe this is expected in a fresh install?). Thanks a lot. Best, Matthias This is the stack trace when I try to install through the web frontend: 141.65.27.89 - - [18/Apr/2017:14:58:19 +] "GET /admin_toolshed/prepare_for_install?changeset_revisions=9ba8ebb636f4_ids=d5dd1c5d2070513e_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu <http://2Ftoolshed.g2.bx.psu.edu>%2F HTTP/1.1" 500 - "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:52.0) Gecko/20100101 Firefox/52.0" Error - : URL: http://bioinf2-dev:8080/admin_toolshed/prepare_for_install?changeset_revisions=9ba8ebb636f4_ids=d5dd1c5d2070513e_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F <http://bioinf2-dev:8080/admin_toolshed/prepare_for_install?changeset_revisions=9ba8ebb636f4_ids=d5dd1c5d2070513e_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F> File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/middleware/error.py', line 154 in __call__ app_iter = self.application(environ, sr_checker) File '/gpfs1/data/galaxy_server/galaxy-dev/.venv/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File '/gpfs1/data/galaxy_server/galaxy-dev/.venv/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__ return self.application(environ, start_response) File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/base.py', line 134 in __call__ return self.handle_request( environ, start_response ) File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/base.py', line 193 in handle_request body = method( trans, **kwargs ) File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/decorators.py', line 98 in decorator return func( self, trans, *args, **kwargs ) File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1035 in prepare_for_install raw_text = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params ) File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/util/__init__.py', line 1488 in url_get response = urlopener.open( full_url ) File '/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/urllib2.py', line 429 in open response = self._open(req, data) File '/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/urllib2.py', line 447 in _open
[galaxy-dev] SSL certificate errors
cursive.include: paste.recursive.include_app_iter: from /> paste.recursive.script_name: '' paste.throw_errors: True request_id: '7599ea98244711e7941208002755efa5' webob._parsed_query_vars: (GET([(u'changeset_revisions', u'9ba8ebb636f4'), (u'repository_ids', u'd5dd1c5d2070513e'), (u'tool_shed_url', u'https://toolshed.g2.bx.psu.edu/')]), 'changeset_revisions=9ba8ebb636f4_ids=d5dd1c5d2070513e_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F') wsgi process: 'Multithreaded' ---- -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- smime.p7s Description: S/MIME Cryptographic Signature ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] drmaa on univa grid engine
Dear list,
I'm struggling to get jobs running on our cluster (UGE).
In the galaxy log I see:
galaxy.jobs.runners.drmaa DEBUG 2017-04-13 12:24:57,799 (10) submitting
file
/gpfs1/data/galaxy_server/galaxy-dev/database/jobs_directory/000/10/galaxy_10.sh
galaxy.jobs.runners.drmaa DEBUG 2017-04-13 12:24:57,799 (10) native
specification is: -l h_rt=60 -l h_vmem=1G -pe smp 2
and I get
galaxy.jobs.runners.drmaa WARNING 2017-04-13 12:24:57,805 (10)
drmaa.Session.runJob() failed, will retry: code 17: error: no suitable
queues
But manual submission works:
qsub -l h_rt=60 -l h_vmem=1G -pe smp 2
/gpfs1/data/galaxy_server/galaxy-dev/database/jobs_directory/000/10/galaxy_10.sh
Your job 161150 ("galaxy_10.sh") has been submitted
So I checked if I can use the drmaa library to submit using the
following python script (based on the example2 included in the library):
"""
#!/usr/bin/env python
from __future__ import print_function
import drmaa
import os
def main():
"""Submit a job.
Note, need file called sleeper.sh in current directory.
"""
s = drmaa.Session()
s.initialize()
print('Creating job template')
jt = s.createJobTemplate()
jt.remoteCommand = os.getcwd() + '/sleeper.sh'
jt.args = ['42','Simon says:']
jt.joinFiles=True
jt.nativeSpecification = "-l h_rt=60 -l h_vmem=1G -pe smp 2"
jobid = s.runJob(jt)
print('Your job has been submitted with id ' + jobid)
print('Cleaning up')
s.deleteJobTemplate(jt)
s.exit()
if __name__=='__main__':
main()
"""
This gives me the same error:
drmaa.errors.DeniedByDrmException: code 17: error: no suitable queues
So it seems to be a problem related to the drmaa python library.
Unfortunately I can not try without any native specs, since time, memory
and cores need to be specifies (a suitable queue is chosen automatically).
I found an earlier post with the same error (but this seemed to be
caused by colons in the file name):
http://dev.list.galaxyproject.org/Galaxy-with-Univa-Grid-Engine-UGE-instead-of-SGE-tt4657848.html#a4657952
Does anyone has suggestions for me?
Best regards,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
smime.p7s
Description: S/MIME Cryptographic Signature
___
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and other Galaxy lists, please use the interface at:
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[galaxy-dev] drmaa chown sudo
Dear galaxy-dev list, The documentation (https://galaxyproject.org/admin/config/performance/cluster/) mentions that sudo permissions for /usr/bin/chown are required in order to run jobs as a real user. This causes quite some headache to our system admins (understandably). I tried (unsuccessfully) to dig a bit in the sources to find the place(s) where sudo chown is called (the idea was to create a small wrapper which might get sudo permissions). But I found that there is already scripts/external_chown_script.py (which is also referred in galaxy.ini). Is it sufficient to make this script sudo callable? Or where could I invoke a wrapper for sudo chown in the galaxy code? Thanks a lot. Best regards, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- smime.p7s Description: S/MIME Cryptographic Signature ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] cluster access
Hi, sorry, I forgot this central piece of information: We also use Univa Grid Engine. What would be easier adapting galaxy's mapping to users or setting up email aliases? I would need to ask our cluster admins if they could realize this. Best, Matthias On 10.04.2017 16:39, Peter Cock wrote: This may depend on the cluster setup, and how Galaxy accesses it. What are you using? We use SGE (actually Univa Grid Engine) via DRMAA, and had to setup usern...@example.org email aliases just for this. Peter On Mon, Apr 10, 2017 at 3:36 PM, Matthias Bernt <m.be...@ufz.de> wrote: Dear list, I'm just starting to get jobs submitted to our cluster as real system user. I read in the documentation that the name of the system user is determined by "the Galaxy user's email address (with the @domain stripped off)". But this does not work on our system, rather the username stored in the galaxy_user table is the name of the user (this is correctly generated by the LDAP login). The job runner script seems to get the user id, so I guess I need to dig deeper. So my question is: Where could I change this behavior? Thanks a lot. Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ -- ------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- smime.p7s Description: S/MIME Cryptographic Signature ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] cluster access
Dear list, I'm just starting to get jobs submitted to our cluster as real system user. I read in the documentation that the name of the system user is determined by "the Galaxy user's email address (with the @domain stripped off)". But this does not work on our system, rather the username stored in the galaxy_user table is the name of the user (this is correctly generated by the LDAP login). The job runner script seems to get the user id, so I guess I need to dig deeper. So my question is: Where could I change this behavior? Thanks a lot. Cheers, Matthias -- --- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann --- smime.p7s Description: S/MIME Cryptographic Signature ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
