[galaxy-dev] Installing galaxy with Apache
Hi, this thread is likely related to this one: http://user.list.galaxyproject.org/Installing-galaxy-with-Apache-td4654499.html I installed Galaxy on a Ubuntu Server 12.04 system. I followed the instruction on the link mentioned above and this one: https://wiki.galaxyproject.org/Admin/Config/ApacheProxy Now my issue is: When I got this configuration in my /etc/apache2/sites-available/default : RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^(.*) http://localhost:8080$1 [P] Galaxy is visible at www.my_server_url.dehttp://www.my_server_url.de but not at www.my_server_url.de/galaxyhttp://www.my_server_url.de/galaxy Following the later URL I got this message: Proxy Error The proxy server received an invalid response from an upstream server. The proxy server could not handle the request GET /galaxyhttp://www.gsa.npz.de/galaxy. Reason: DNS lookup failure for: localhost:8080http: Apache/2.2.22 (Ubuntu) Server at www.my_server_url.de Port 80 When I change the configuration like this: (make the second line a comment): RewriteEngine on #RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^(.*) http://localhost:8080$1 [P] Galaxy is visible both at www.my_server_url.dehttp://www.my_server_url.de and at www.my_server_url.de/galaxyhttp://www.my_server_url.de/galaxy When I completely remove this part, the It works! standard page of apache is displayed. The configuration in my universe.ini is as follows: host = 127.0.0.1 [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy [app:main] filter-with = proxy-prefix cookie_path = /galaxy Can you please help me with this issue? I want to see the It works! page at www.my_server_url.dehttp://www.my_server_url.de and galaxy only at www.my_server_urla.de/galaxy. Thanks in advance! Kind regards Matthias Enders ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Cluster Admins - Call for experiences/issues encountered
Hi Eric, thanks for caring about that issue. Do you know about Galaxy Community Hubs? https://wiki.galaxyproject.org/Community/ The community is encouraged to share experience under that page. Maybe you can add yours to that page as well? Cheers, Bjoern Am 27.05.2014 18:32, schrieb Eric Rasche: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 This is specifically to galaxy administrators and developers who have worked with galaxy and cluster deployment. If you have successfully deployed a galaxy instance backed by one (or more) clusters, I'm looking to hear about your experience; - - the configuration - - any pitfalls encountered - - any extra tools that needed to be installed - - any ugly hacks you had to implement The current cluster documentation is somewhat lacking, and I'm willing to compile everyone's experiences deploying to clusters if you're willing to send them in. I'll update the cluster page on the wiki as I receive replies and can allocate time. By way of example, here's the summary of what I would reply to this email with my experiences deploying to an HTCondor cluster - - HTcondor ran fine, accepted jobs and worked for all users - - Connecting galaxy to it would result in some jobs running/some jobs failing. It was determined that those jobs which ran, were only on localhost. - - This was a result of the fact that galaxy's home directory/data was not exported - - Galaxy was made an LDAP user and a folder created in the correct location on all computers - - This still failed, as galaxy does not transfer files by default (as far as I can tell), even though that's available in HTCondor - - Finally galaxy's home directory was NFS exported and things seemed to work. Cheers, Eric - -- Eric Rasche Programmer II Center for Phage Technology Texas AM University College Station, TX 77843 404-692-2048 e...@tamu.edu rasche.e...@yandex.ru -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.17 (GNU/Linux) iQIcBAEBAgAGBQJThL4PAAoJEMqDXdrsMcpVJ0wP/jPFrTxRYnWcavbUxhht8tWE VDhid2pst7o+qkkLAUylPyNzJz31movsU1Gd2FJLP4+RHb3lhy2GWm8mR9G4JuMM g7fHAwIRj1qTT5tMXAEN6EoCtrValZH0EkIQPaFUPIiN1wzGTTDP56V+L6f3xQNg zglk2GTO+hM+AunYGuDugDvdKTPyKgR1K2vaCNdc2kZlvQZe7TlOHZEbXaoDGTY4 vwHcNR0+8fvf6Hs1liCuCuh8nlTBABZLxMl5LgxOaZqbaAVQWsqXNdh1tF/rlERL +PlNv5HRBWz26iGE04jbAD1pKmxg33Knl3l4MXrUnB5ZJ2dIDJL0YHOhXM3mjI4T Hf8mv/iVr21xx3zrrAbAlRIt3Npw4DtaGSqBFdKvnxQZygjKEF7ZKTGfA4xLNRHh 4dPElUpv8b3jUe2GqhXyrmHYuBdWqBC5Y/ii0k4c/bHjoXW6yg0mPs7po7i5+5JS wnO3mfoFhnyEALd45EBprkQY+kx05zjSg4ntpeywl8fIM2uGT0GyANA0/prKhcmB 5PiYUejsaDTY4GigiiZqz0tnC5z7VDyjByfyl7ufNaaCWNRXlTNIzH0ePy0ZjLrU Sj8XyI1XoOSdtyxxvNNe8OPDxxffnJxi0rres4Q3CC/EbZK4vBF7chsisHd28Q29 M1e+lNdO8FBIoy5+MR3H =6Jbk -END PGP 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] stdout in history
Hi All, I think it makes a lot of sense to allow disabling the addition of stderr and/or stdout to dataset.info on a per tool/output dataset basis. I’ve added a Trello card for this here: https://trello.com/c/hC5HABnr. Not sure when anyone might have a chance to look into it, but pull requests are always welcome. Thanks for using Galaxy, Dan On May 31, 2014, at 11:12 AM, Jorrit Boekel jorrit.boe...@scilifelab.se wrote: Hi Neil, I had some problems with this before too, so I created an tool config option a long time ago in my own galaxy fork. Never really bothered with submitting it, but it lives in these commits: https://bitbucket.org/glormph/adapt/commits/4ba256a9b8782642429ecb5472a456584bed86d5 https://bitbucket.org/glormph/adapt/commits/86ec8b1cfeb737dfa31a1b6faf18d918bea7b4c3 I started implementing it in datatypes (first commit), but moved it to tool config instead. If this is really interesting I guess I can submit a pull request, but it felt a bit hacky at the time. cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden On 30 May 2014, at 14:35, neil.burd...@csiro.au wrote: Hi, It seems that the first 4/5 lines that are printed in the source code tools appear in the history (when expended) and in stdout link. Is there anyway to stop print statements appearing in the history panel? Thanks Neil ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Cluster Admins - Call for experiences/issues encountered
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Bjoern, Yes, I am aware of such. I had intended to update the Cluster docs as it's the more appropriate page, perhaps linking to it from the community log page. I was hoping that people might send in their experiences so I could aggregate them and write the entries for them. There's always a lot of apathy towards documentation, and given that this is a feature used by a select few (even if many organisations use it, only a handful of people are actually doing the deployment), I figured that they might be more easily convinced to simply summarise their issues/experiences in a dozen bulletpoints. Additionally by aggregation we could easily identify common problems and highlight those for others to see. That said...no one has replied to this yet. I fully intend to at least include mine, however I was holding out for some other replies. Cheers, Eric On 06/02/2014 08:55 AM, Björn Grüning wrote: Hi Eric, thanks for caring about that issue. Do you know about Galaxy Community Hubs? https://wiki.galaxyproject.org/Community/ The community is encouraged to share experience under that page. Maybe you can add yours to that page as well? Cheers, Bjoern Am 27.05.2014 18:32, schrieb Eric Rasche: This is specifically to galaxy administrators and developers who have worked with galaxy and cluster deployment. If you have successfully deployed a galaxy instance backed by one (or more) clusters, I'm looking to hear about your experience; - the configuration - any pitfalls encountered - any extra tools that needed to be installed - any ugly hacks you had to implement The current cluster documentation is somewhat lacking, and I'm willing to compile everyone's experiences deploying to clusters if you're willing to send them in. I'll update the cluster page on the wiki as I receive replies and can allocate time. By way of example, here's the summary of what I would reply to this email with my experiences deploying to an HTCondor cluster - HTcondor ran fine, accepted jobs and worked for all users - Connecting galaxy to it would result in some jobs running/some jobs failing. It was determined that those jobs which ran, were only on localhost. - This was a result of the fact that galaxy's home directory/data was not exported - Galaxy was made an LDAP user and a folder created in the correct location on all computers - This still failed, as galaxy does not transfer files by default (as far as I can tell), even though that's available in HTCondor - Finally galaxy's home directory was NFS exported and things seemed to work. Cheers, Eric ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ - -- Eric Rasche Programmer II Center for Phage Technology Texas AM University College Station, TX 77843 -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQIcBAEBAgAGBQJTjI4NAAoJEMqDXdrsMcpVk5YP+waHzbx5MS3g31a3l7hC+84M g0jakKQM2t6A/516q3YTm3FouGFpitcvxXYaesDDr/AbiRSWY8KGX6nqn8xk4LNH yxc2Unewfwuzo8hB+PGHUncRnYAIc+BSDr57BDQukY7cuSBV6dymKkipXyim3v3Z buLFKkby17SAvCmBxHN6cfGKnRs6ZLCh0qAyZaTWwmTmrqg3gY3WUh7jBsIS0qUV bMEomgQ4vmqsOoEhi2UsA3ph09y8XcmyQCOkKLcR8nszvRcH/3s89YdMScxs9ghU nGdVaO6B3zXG9QnWc8XgokISCldTcsP5GkKUPcMayz5n9tx2+Mf+BZQdQpGU7qQe P5hGX0sJstklN1TRoJgvR/e6GBaEfT3yPgHlEi+1L7vlrb57vPYXi2Empph/KYo/ fUKGS0q2joxcg3/z2MNzrHc5+y+H9wR0dYVZrUEn3VBY+bhvaIdwpA4BBjjSjf99 BcvUk7FIKi6eyhCFX8RzU8CF4mXNqtrSXzd26igL8datxW0y7bhYcfiied0RMFQv zz6Q4fQyV8hz5ufXKyf7Z1fJ+0PqIiGotN1/wD/l09mMFoKqJhvs4510LhCv7WW+ K7/KBJWJ2O8GrcuW4z7vydF+FxRLpkfGERzKI9IeMmxJiAs8OSYmIROsQzxg7alD MEHRwJf6505DZSTeFDTn =qHdv -END PGP 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Cluster Admins - Call for experiences/issues encountered
Hi, Yes, I am aware of such. I had intended to update the Cluster docs as it's the more appropriate page, perhaps linking to it from the community log page. I was hoping that people might send in their experiences so I could aggregate them and write the entries for them. There's always a lot of apathy towards documentation, and given that this is a feature used by a select few (even if many organisations use it, only a handful of people are actually doing the deployment), I figured that they might be more easily convinced to simply summarise their issues/experiences in a dozen bulletpoints. Additionally by aggregation we could easily identify common problems and highlight those for others to see. That is always good, yes, but hard to motivate people. My problem is that I do not remember every detail of every problem, it's to far away. Galaxy is running for us now. But if I encounter any new problem I will let you and the wiki know. That said...no one has replied to this yet. I fully intend to at least include mine, however I was holding out for some other replies. Fingers crossed! Bjoern Cheers, Eric On 06/02/2014 08:55 AM, Björn Grüning wrote: Hi Eric, thanks for caring about that issue. Do you know about Galaxy Community Hubs? https://wiki.galaxyproject.org/Community/ The community is encouraged to share experience under that page. Maybe you can add yours to that page as well? Cheers, Bjoern Am 27.05.2014 18:32, schrieb Eric Rasche: This is specifically to galaxy administrators and developers who have worked with galaxy and cluster deployment. If you have successfully deployed a galaxy instance backed by one (or more) clusters, I'm looking to hear about your experience; - the configuration - any pitfalls encountered - any extra tools that needed to be installed - any ugly hacks you had to implement The current cluster documentation is somewhat lacking, and I'm willing to compile everyone's experiences deploying to clusters if you're willing to send them in. I'll update the cluster page on the wiki as I receive replies and can allocate time. By way of example, here's the summary of what I would reply to this email with my experiences deploying to an HTCondor cluster - HTcondor ran fine, accepted jobs and worked for all users - Connecting galaxy to it would result in some jobs running/some jobs failing. It was determined that those jobs which ran, were only on localhost. - This was a result of the fact that galaxy's home directory/data was not exported - Galaxy was made an LDAP user and a folder created in the correct location on all computers - This still failed, as galaxy does not transfer files by default (as far as I can tell), even though that's available in HTCondor - Finally galaxy's home directory was NFS exported and things seemed to work. Cheers, Eric ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ - -- Eric Rasche Programmer II Center for Phage Technology Texas AM University College Station, TX 77843 -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQIcBAEBAgAGBQJTjI4NAAoJEMqDXdrsMcpVk5YP+waHzbx5MS3g31a3l7hC+84M g0jakKQM2t6A/516q3YTm3FouGFpitcvxXYaesDDr/AbiRSWY8KGX6nqn8xk4LNH yxc2Unewfwuzo8hB+PGHUncRnYAIc+BSDr57BDQukY7cuSBV6dymKkipXyim3v3Z buLFKkby17SAvCmBxHN6cfGKnRs6ZLCh0qAyZaTWwmTmrqg3gY3WUh7jBsIS0qUV bMEomgQ4vmqsOoEhi2UsA3ph09y8XcmyQCOkKLcR8nszvRcH/3s89YdMScxs9ghU nGdVaO6B3zXG9QnWc8XgokISCldTcsP5GkKUPcMayz5n9tx2+Mf+BZQdQpGU7qQe P5hGX0sJstklN1TRoJgvR/e6GBaEfT3yPgHlEi+1L7vlrb57vPYXi2Empph/KYo/ fUKGS0q2joxcg3/z2MNzrHc5+y+H9wR0dYVZrUEn3VBY+bhvaIdwpA4BBjjSjf99 BcvUk7FIKi6eyhCFX8RzU8CF4mXNqtrSXzd26igL8datxW0y7bhYcfiied0RMFQv zz6Q4fQyV8hz5ufXKyf7Z1fJ+0PqIiGotN1/wD/l09mMFoKqJhvs4510LhCv7WW+ K7/KBJWJ2O8GrcuW4z7vydF+FxRLpkfGERzKI9IeMmxJiAs8OSYmIROsQzxg7alD MEHRwJf6505DZSTeFDTn =qHdv -END PGP 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] New tool on TestToolShed still not tested
Peter, Thank you for reporting this issue, which should be resolved in 13703:8caa7f4d72c7. Tonight's test run should correctly install and test blast_rbh. --Dave B. On Tue 27 May 2014 10:23:15 AM EDT, Peter Cock wrote: Thanks - I'll leave this until next week then. Peter On Tue, May 27, 2014 at 3:05 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello peter, I've looked inot this and discovered what I suspect is a problem with the buildbot configuration for the Tool Shed's install and test framework. The framework is executed in 2 stages where stage 1 installs and tests repositories that contain tool dependency packages, and stage 2 installs and test repositories that contain tools the require them. For the past few test runs, only stage 1 executes, so no repositories that contain tools are tested (this affects all stage 2 repositories, not just yours). The buildbot environment is Dave B's realm (I've not been involved in setting it up), so he'll have to take a look to see what may be the problem. Unfortunately, Dave is out of the lab this week, so we'll have to wait until next week to get this resolved. Sorry for the inconvenience on this, and the unfortunate timing with Dave being out. I've added the following Trello card for this issue: https://trello.com/c/YElEsCWl/208-install-and-test-framework-stage-2-does-not-run Greg Von Kuster On May 26, 2014, at 6:46 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi guys, I updated this new tool on Wednesday last week, but it still has no functional test results: http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_rbh Has it been excluded for some reason? If so, could some indicator be shown (at least to the tool authors)? I looked over some of my other tools and the test dates are quite variable. I thought you had gone from nightly tests to every second night - but is the scheme now more complex, or have there been technical difficulties? Thanks, Peter ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tool dependencies fail
I tried requirements requirement type=packagehhsuite/requirement /requirements and that had no effect. I. -- Message: 3 Date: Sat, 31 May 2014 03:51:55 +0200 From: Bj?rn Gr?ning bjoern.gruen...@gmail.com To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] tool dependencies fail Message-ID: 538935bb.7020...@gmail.com Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi, can you try: requirements requirement type=packagehhsuite/requirement /requirements Hope that helps, sorry for the short answer I'm too tired :) Bjoern ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tool dependencies fail
Hello Dave, I got interrupted before I could reply to the second suggestion from Jorrit: Not sure about specifying the absolute path for the tool dependency dir, but I always use it. using the absolute path of the tool dependency dir had no effect. Also, my env.sh neither has a #!/bin/bash shebang line, nor quote marks around the tool path. Removed shebang, quote marks (these are in the wiki example): no effect. If you are in the hhsuite/default/ dir and source env.sh, can you then run hhblits yourself (as galaxy user, or whoever owns the tools)? This helped: it looks like I had to specify an additional env variable HHDIR to make it work. So definitely making progress. However, the error was not that the executable was not found, but that HHDIR was missing. I now know I have to use the env.sh BUT: galaxy is not sourcing env.sh. That is my problem. I am confused by your question: if I go with the env.sh solution, I am assuming I do not need to create a 'default' directory and do not need the requirement tag. Is this correct? Isabelle On 6/2/14 10:34 AM, Dave Bouvier d...@bx.psu.edu wrote: Isabelle, In order to help track down the cause of this issue, could you provide the output of the following two commands? ls -lh tool_dependencies/hhsuite/ ls -lh tool_dependencies/hhsuite/default/ --Dave B. On Mon 02 Jun 2014 01:29:44 PM EDT, Isabelle Phan wrote: I tried requirements requirement type=packagehhsuite/requirement /requirements and that had no effect. I. -- Message: 3 Date: Sat, 31 May 2014 03:51:55 +0200 From: Bj?rn Gr?ning bjoern.gruen...@gmail.com To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] tool dependencies fail Message-ID: 538935bb.7020...@gmail.com Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi, can you try: requirements requirement type=packagehhsuite/requirement /requirements Hope that helps, sorry for the short answer I'm too tired :) Bjoern ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tool dependencies fail
Galaxy is not sourcing env.sh I tried sourcing it before restarting galaxy and it worked. So that's the issue. How do I get galaxy to source env.sh? $ ls -lh tool_dependencies/hhsuite/ total 8 drwxr-xr-x@ 11 iphan SBRI\Domain Users 374B Jun 2 10:54 2.0.16/ lrwxr-xr-x 1 iphan SBRI\Domain Users 7B Jun 2 10:54 default@ - 2.0.16/ $ $ ls -lh tool_dependencies/hhsuite/default/ total 784 -rw-r--r--@ 1 iphan SBRI\Domain Users20K Mar 19 2013 CHANGES -rw-r--r--@ 1 iphan SBRI\Domain Users36K Mar 19 2013 LICENSE -rw-r--r--@ 1 iphan SBRI\Domain Users 6.0K Mar 19 2013 README drwxr-xr-x@ 10 iphan SBRI\Domain Users 340B May 30 13:18 bin/ -rwxrwxrwx+ 1 iphan SBRI\Domain Users 186B Jun 2 10:54 env.sh* -rw-r--r--@ 1 iphan SBRI\Domain Users 319K Mar 19 2013 hhsuite-userguide.pdf drwxr-xr-x@ 3 iphan SBRI\Domain Users 102B May 30 13:18 include/ drwxr-xr-x@ 6 iphan SBRI\Domain Users 204B May 30 13:20 lib/ thanks, Isabelle On 6/2/14 10:50 AM, Isabelle Phan isabelle.p...@seattlebiomed.org wrote: Hello Dave, I got interrupted before I could reply to the second suggestion from Jorrit: Not sure about specifying the absolute path for the tool dependency dir, but I always use it. using the absolute path of the tool dependency dir had no effect. Also, my env.sh neither has a #!/bin/bash shebang line, nor quote marks around the tool path. Removed shebang, quote marks (these are in the wiki example): no effect. If you are in the hhsuite/default/ dir and source env.sh, can you then run hhblits yourself (as galaxy user, or whoever owns the tools)? This helped: it looks like I had to specify an additional env variable HHDIR to make it work. So definitely making progress. However, the error was not that the executable was not found, but that HHDIR was missing. I now know I have to use the env.sh BUT: galaxy is not sourcing env.sh. That is my problem. I am confused by your question: if I go with the env.sh solution, I am assuming I do not need to create a 'default' directory and do not need the requirement tag. Is this correct? Isabelle On 6/2/14 10:34 AM, Dave Bouvier d...@bx.psu.edu wrote: Isabelle, In order to help track down the cause of this issue, could you provide the output of the following two commands? ls -lh tool_dependencies/hhsuite/ ls -lh tool_dependencies/hhsuite/default/ --Dave B. On Mon 02 Jun 2014 01:29:44 PM EDT, Isabelle Phan wrote: I tried requirements requirement type=packagehhsuite/requirement /requirements and that had no effect. I. -- Message: 3 Date: Sat, 31 May 2014 03:51:55 +0200 From: Bj?rn Gr?ning bjoern.gruen...@gmail.com To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] tool dependencies fail Message-ID: 538935bb.7020...@gmail.com Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi, can you try: requirements requirement type=packagehhsuite/requirement /requirements Hope that helps, sorry for the short answer I'm too tired :) Bjoern ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Uploading files to galaxy from a folder
John, For us, it's not just a question of deleting the file, but of having permission to do python's copystat (see stack trace below). We've tried a variety of permission combinations, including sticky group permissions, various setfacl's and moving the directory on or off the same filesystem as the dataset storage, but still haven't arrived a happy solution. I also looked into Iyad earlier posting of a patch up upload.py, but in our configuration, upload.py runs on the compute nodes (not the galaxy head node) where the galaxy user does NOT have sudo previleges, so we really need a solution that does the chown further up the food chain - before the job is queued. I'm guessing it should go somewhere in lib/galaxy/tools/actions/upload_common.py, but I haven't had time to come to grips with this code yet - any suggestions would be welcome. That code already has the sudo chown for running jobs as their real user (at least on my somewhat dated codebase), so I'm thinking that same external_chown script could also be used for this purpose (chown before import). Regards, Curtis Traceback (most recent call last): File /share/apps/galaxy/galaxy-rollouttest/tools/data_source/upload.py, line 401, in module __main__() File /share/apps/galaxy/galaxy-rollouttest/tools/data_source/upload.py, line 390, in __main__ add_file( dataset, registry, json_file, output_path ) File /share/apps/galaxy/galaxy-rollouttest/tools/data_source/upload.py, line 270, in add_file line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place ) File /share/apps/galaxy/galaxy-rollouttest/lib/galaxy/datatypes/sniff.py, line 106, in convert_newlines shutil.move( temp_name, fname ) File /share/apps/galaxy/python/2.6.6/lib/python2.6/shutil.py, line 260, in move copy2(src, real_dst) File /share/apps/galaxy/python/2.6.6/lib/python2.6/shutil.py, line 96, in copy2 copystat(src, dst) File /share/apps/galaxy/python/2.6.6/lib/python2.6/shutil.py, line 66, in copystat os.utime(dst, (st.st_atime, st.st_mtime)) OSError: [Errno 1] Operation not permitted: '/scratch/importfs/galaxy/sunnie/1-5.txt' -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Kandalaft, Iyad Sent: Sunday, June 01, 2014 7:31 PM To: John Chilton Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Uploading files to galaxy from a folder Hi John I will review the galaxy code more closely and implement it as you suggested. It's been a while since I've implemented this 'fix', so I will have to dig up the code that tries to delete the file after upload. Once it's simple and clean, I will do a pull request. Thanks for your input. Iyad Kandalaft Bioinformatics Programmer Microbial Biodiversity Bioinformatics Science Technology Branch Agriculture Agri-Food Canada iyad.kandal...@agr.gc.ca | (613) 759-1228 From: John Chilton [jmchil...@gmail.com] Sent: June 1, 2014 7:53 PM To: Kandalaft, Iyad Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Uploading files to galaxy from a folder Hello Iyad, Thanks for taking the time to describe your problem and share your solution - I am sure other institutions have desires to harness the ftp upload option the way you are doing it. Is the only problem that occurs if the ownership is incorrect that Galaxy cannot delete the files? If so - I feel like as a deployer I would prefer to have a sudo script that just deletes the files instead of changing the ownership? It is a more... focused sudo command. This strategy could also allow a slightly more general universe_wsgi.ini option - say a few options such as: ftp_upload_delete_handling = __default__ # just assume ownership and delete ftp_upload_delete_handling = __none__ # don't delete files - user is responsible ftp_upload_delete_handling = sudo -E rm # command prefix to delete file I am not saying if you clean up what you have and opened a pull request I would say no - I am just saying I would be more eager for this more general option. If you can confirm the only reason the permissions need to change is to delete the files and likewise prefer this variant but cannot figure out how to modify upload.py - let me know I can try to look into it (no promises that it is easy to implement). -John On Tue, May 27, 2014 at 10:28 AM, Kandalaft, Iyad iyad.kandal...@agr.gc.ca wrote: Hi Everyone I'm throwing this out there for some feedback and recommendations. Objective: Facilitate transferring large files ( 2GB) from an HPC cluster (and its associated fast tier storage) to galaxy for my clients. I enabled the FTP upload option in galaxy but it involves users learning to copy files over FTP. So, I created a galaxy folder in each users' home directory on the HPC Cluster that symbolically links to the FTP upload folder for galaxy. Hence,
Re: [galaxy-dev] Uploading files to galaxy from a folder
Iyad, Yes, that's a different topology. We run on a shared cluster, so the Galaxy head nodes (app + db) sit next to the cluster, and the galaxy user has no special powers outside the head node, though the filesystem is completely cross-mounted. Regards, Curtis -Original Message- From: Kandalaft, Iyad [mailto:iyad.kandal...@agr.gc.ca] Sent: Monday, June 02, 2014 2:01 PM To: Curtis Hendrickson (Campus); John Chilton Cc: galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] Uploading files to galaxy from a folder Hi Curtis, I recall coming across the external chown script you mentioned but for some reason it wasn't working as expected, which is why I opted to insert in my own function in upload.py. I think the documentation in the universe_wsgi.ini didn't match up with how the script worked, so I didn't bother trying to find that functionality in the code. I suppose that you are suggesting that my codebase is somewhat proprietary to our environment, which is correct. On our cluster at AAFC, the headnode, which differs from the galaxy server, can sync any file across the entire cluster (such as /etc/sudoers.d/galaxy). Hence, I can propagate sudo permissions from the headnode to the compute nodes. Alternatively, I opted to set the upload script to execute locally on the galaxy server as you implied. I will review the codebase related to the original chown script and see if it needs any tweaking (or maybe just better documented). Regards, Iyad Kandalaft Bioinformatics Application Developer Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada KW Neatby Bldg | éd. KW Neatby 960 Carling Ave| 960, avenue Carling Ottawa, ON | Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel: iyad.kandal...@agr.gc.ca Telephone | Téléphone 613- 759-1228 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada -Original Message- From: Curtis Hendrickson (Campus) [mailto:curt...@uab.edu] Sent: Monday, June 02, 2014 2:27 PM To: Kandalaft, Iyad; John Chilton Cc: galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] Uploading files to galaxy from a folder John, For us, it's not just a question of deleting the file, but of having permission to do python's copystat (see stack trace below). We've tried a variety of permission combinations, including sticky group permissions, various setfacl's and moving the directory on or off the same filesystem as the dataset storage, but still haven't arrived a happy solution. I also looked into Iyad earlier posting of a patch up upload.py, but in our configuration, upload.py runs on the compute nodes (not the galaxy head node) where the galaxy user does NOT have sudo previleges, so we really need a solution that does the chown further up the food chain - before the job is queued. I'm guessing it should go somewhere in lib/galaxy/tools/actions/upload_common.py, but I haven't had time to come to grips with this code yet - any suggestions would be welcome. That code already has the sudo chown for running jobs as their real user (at least on my somewhat dated codebase), so I'm thinking that same external_chown script could also be used for this purpose (chown before import). Regards, Curtis Traceback (most recent call last): File /share/apps/galaxy/galaxy-rollouttest/tools/data_source/upload.py, line 401, in module __main__() File /share/apps/galaxy/galaxy-rollouttest/tools/data_source/upload.py, line 390, in __main__ add_file( dataset, registry, json_file, output_path ) File /share/apps/galaxy/galaxy-rollouttest/tools/data_source/upload.py, line 270, in add_file line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place ) File /share/apps/galaxy/galaxy-rollouttest/lib/galaxy/datatypes/sniff.py, line 106, in convert_newlines shutil.move( temp_name, fname ) File /share/apps/galaxy/python/2.6.6/lib/python2.6/shutil.py, line 260, in move copy2(src, real_dst) File /share/apps/galaxy/python/2.6.6/lib/python2.6/shutil.py, line 96, in copy2 copystat(src, dst) File /share/apps/galaxy/python/2.6.6/lib/python2.6/shutil.py, line 66, in copystat os.utime(dst, (st.st_atime, st.st_mtime)) OSError: [Errno 1] Operation not permitted: '/scratch/importfs/galaxy/sunnie/1-5.txt' -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Kandalaft, Iyad Sent: Sunday, June 01, 2014 7:31 PM To: John Chilton Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Uploading files to galaxy from a folder Hi John I will review the galaxy code more closely and implement it as you suggested. It's been a while since I've implemented this 'fix', so I will have to dig up the code that tries to delete the file after upload. Once it's simple and clean, I will do a pull request. Thanks for your input. Iyad Kandalaft Bioinformatics Programmer Microbial
Re: [galaxy-dev] Unable to access admin after install EMBOSS 5 from galaxy test repo
Hello Cristian, I've just instaled the emboss_5 repository along with all dependencies from the test Tool Shed, so I'm not sure what configuration in your Galaxy environment may be causing the behavior you're seeing. Currently the only way to uninstall a repository is via the Galaxy admin UI. There is a Trello card here to enhance the Galaxy API to support uninstalling a repository, but the featue is not yet implemented: https://trello.com/c/4VktpvTd/207-enhance-the-galaxy-api-for-the-tool-shed-to-allow-uninstalling-a-repository Sorry for the inconvenience! Greg Von Kuster On Jun 1, 2014, at 2:32 PM, Cristian Alejandro Rojas alejandro.0...@gmail.com wrote: Hello all, I've select the emboss 5 suite to install from Galaxy test repo. After install I cant access to the admin panel. I think that is beacuse the json value is not complete (len(value):65535), and therefore the json decoder cant decode the value. In attachments I have included the debug data generated by galaxy and the file containing the value variable. Can anybody bring me some help? Is there some way to remove emboss without using the admin panel? Thanks in advance, best regards. Cristian Alejandro Rojas Quintero error_galaxy.txterror_galaxy.xmlerror_galaxy_extra_data.txtjson_value.txt___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] June 2, 2014 Galaxy Distribution
June 2, 2014 Galaxy Distribution http://wiki.galaxyproject.org/News/2014_06_02_Galaxy_Distribution *News Brief http://wiki.galaxyproject.org/DevNewsBriefs/2014_06_02**Highlights:* * Dataset Collections introduced * Changes to database build (dbkey) organization * Enhancements to Tool configuration and Workflow options * Trackster, User Interface, and Admin panel upgrades * Significant updates to Admin and Job functionality * Tool Shed repository and API additions * Data updates plus new Security features and Bug fixes * new*: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable *upgrade*: $ hg pull $ hg update latest_2014.06.02 getgalaxy.org http://wiki.galaxyproject.org/Admin/Get%20Galaxy galaxy-dist.readthedocs.org http://galaxy-dist.readthedocs.org/ bitbucket.org/galaxy/galaxy-dist http://bitbucket.org/galaxy/galaxy-dist* * /Thanks for using Galaxy!/ The Galaxy Team http://wiki.galaxyproject.org/GalaxyTeam ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] visulaization of tree produced by raxml
Hi, Do you guys have any suggestions on what tool I should use to construct tree from the output produces by raxml. There are some tree builder in Galaxy that seem not to be working with this output (correct me if I am wrong). The developer of raxml recommend dendroscope which is not available in Galaxy. Any suggestions are welcomed, Philip ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
