[galaxy-dev] Bowtie2 error: Creates a 62 kb file.
Dear all, Today we ran some problems when running bowtie2. When we run bowtie2, the run manages to complete. However, bowtie2 creates a 62kb file. The error log that we get is the following: galaxy.jobs DEBUG 2013-07-23 17:09:42,378 (1483) Persisting job destination (destination id: local:///) galaxy.jobs.handler INFO 2013-07-23 17:09:42,392 (1483) Job dispatched galaxy.tools DEBUG 2013-07-23 17:09:42,556 Building dependency shell command for dependency 'bowtie2' galaxy.tools WARNING 2013-07-23 17:09:42,556 Failed to resolve dependency on 'bowtie2', ignoring galaxy.tools DEBUG 2013-07-23 17:09:42,556 Building dependency shell command for dependency 'samtools' galaxy.tools WARNING 2013-07-23 17:09:42,556 Failed to resolve dependency on 'samtools', ignoring galaxy.jobs.runners.local DEBUG 2013-07-23 17:09:42,626 (1483) executing: bowtie2 --version /usr/local/galaxy/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_1483; python /usr/local/galaxy/galaxy-dist/tools/sr_mapping/bowtie2_wrapper.py --num-threads=4 --output=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1673.dat --indexes-path=/data/db/fungidb/Ncrassa_OR74A/bowtie2/Ncrassa_wt_Chr01.Chr07.+ChrM.+rDNA_v12 --single-paired=paired --input1=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1668.dat --input2=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1669.dat -I 0 -X 250 --settings=preSet galaxy.jobs DEBUG 2013-07-23 17:09:42,696 (1483) Persisting job destination (destination id: local:///) galaxy.jobs.runners.local DEBUG 2013-07-23 17:09:42,766 execution finished: bowtie2 --version /usr/local/galaxy/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_1483; python /usr/local/galaxy/galaxy-dist/tools/sr_mapping/bowtie2_wrapper.py --num-threads=4 --output=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1673.dat --indexes-path=/data/db/fungidb/Ncrassa_OR74A/bowtie2/Ncrassa_wt_Chr01.Chr07.+ChrM.+rDNA_v12 --single-paired=paired --input1=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1668.dat --input2=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1669.dat -I 0 -X 250 --settings=preSet galaxy.jobs.runners DEBUG 2013-07-23 17:09:42,850 executing external set_meta script for job 1483: /usr/local/galaxy/galaxy-dist/set_metadata.sh ./database/files /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483 . /usr/local/galaxy/galaxy-dist/universe_wsgi.ini /usr/local/galaxy/galaxy-dist/database/tmp/tmpUiqpPD /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/galaxy.json /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_in_HistoryDatasetAssociation_1767_wqhEmr,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_kwds_HistoryDatasetAssociation_1767_qVZjpG,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_out_HistoryDatasetAssociation_1767_vIfpRO,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_results_HistoryDatasetAssociation_1767_UNl6OR,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_over! ride_HistoryDatasetAssociation_1767_MZilrL 165.91.11.135 - - [23/Jul/2013:17:09:43 -0500] GET /api/histories/ca8efa3c47500414 HTTP/1.1 200 - http://galaxy.tamu.edu/history; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.22 (KHTML, like Gecko) Ubuntu Chromium/25.0.1364.160 Chrome/25.0.1364.160 Safari/537.22 165.91.11.231 - - [23/Jul/2013:17:09:43 -0500] GET /history HTTP/1.1 200 - http://galaxy.tamu.edu/tool_runner/index; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.71 Safari/537.36 165.91.11.231 - - [23/Jul/2013:17:09:43 -0500] GET /api/histories/1ab12f1e464820dd HTTP/1.1 200 - http://galaxy.tamu.edu/history; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.71 Safari/537.36 165.91.11.231 - - [23/Jul/2013:17:09:43 -0500] GET /history/get_display_application_links HTTP/1.1 200 - http://galaxy.tamu.edu/history; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.71 Safari/537.36 galaxy.jobs.runners DEBUG 2013-07-23 17:09:44,457 execution of external set_meta for job 1483 finished galaxy.datatypes.metadata DEBUG 2013-07-23 17:09:44,545 loading metadata from file for: HistoryDatasetAssociation 1767 We currently have the most recent version of bowtie2 and samtools. Anyone know how to fix this? Thank you for your time, --Ricardo Perez ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to
[galaxy-dev] GATK fasta file missing ERROR
Dear Developers, I am GATK (beta ) Unified Genotyper module to get the indels and SNP. I placed the jar file in (/galaxy-dist/tool-data/shared/jars/gatk) and i link the reference genome in .loc file (gatk_sorted_picard_index.loc). I could see the Name i mentioned in the .loc file is appearing in the galaxy page while choosing the Reference genome. Now while running GATK in galaxy , The command runs for a while and gives ERROR as i am getting ERROR as *(The fasta file you specified (/tmp/tmp-gatk-Jjg9Mi) does not exist.)* Could anybody suggest on the same.. Thanks Sridhar ___ 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] tool input is folder rather than file
Dear Developers, I want to design a tool whose input is folder containing files and sub-folders. I was wandering which value should I assign to TYPE attribute of PARAM tag in INPUTS. -- Best regards, Pankaj Narang ___ 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] Disable cheetah filtering
Hi all, A Cheetah question: when I enter ; as a value in a text box of a tool (stored in $exp), Cheetah prints this as X, and passed this string to the tool. How to disable this behaviour in Cheetah? I have tried to play with #filter directives, but to no avail. Thanks, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team ___ 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] Disable cheetah filtering
Hi Joachim, try that one: http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_set Cheers, Bjoern Hi all, A Cheetah question: when I enter ; as a value in a text box of a tool (stored in $exp), Cheetah prints this as X, and passed this string to the tool. How to disable this behaviour in Cheetah? I have tried to play with #filter directives, but to no avail. Thanks, Joachim ___ 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] Disable cheetah filtering
On Wed, Jul 24, 2013 at 9:40 AM, Joachim Jacob | VIB | joachim.ja...@vib.be wrote: Hi all, A Cheetah question: when I enter ; as a value in a text box of a tool (stored in $exp), Cheetah prints this as X, and passed this string to the tool. How to disable this behaviour in Cheetah? I have tried to play with #filter directives, but to no avail. Thanks, Joachim That sounds like the Galaxy character sanitation making the change, things like pipes etc can have unexpected results in command lines. Have a look at the sanitizer tag for use in the tool's XML file. 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/
[galaxy-dev] All processes are freezed
Hi everybody Since yesterday all processes I have run on Galaxy main are waiting. The system displayed a message to contact a Galaxy admin, but I could find no other way rather than this mailing list. Is this freeze due to a public maintenance, or it's just my problem? Best wishes, Ali ___ 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] Disable cheetah filtering
Thanks both of you! Okay, so I was looking in the wrong direction. This solved the issue. Cheers, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 07/24/2013 11:13 AM, Björn Grüning wrote: Hi Joachim, try that one: http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_set Cheers, Bjoern Hi all, A Cheetah question: when I enter ; as a value in a text box of a tool (stored in $exp), Cheetah prints this as X, and passed this string to the tool. How to disable this behaviour in Cheetah? I have tried to play with #filter directives, but to no avail. Thanks, Joachim ___ 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] Disable cheetah filtering
Okay, normally I would have forked the galaxy-dist and do a pull request with my change. But the change I want to commit is in the tool 'add_value', which is in the toolshed. Seems like a safer approach to me to contribute to the toolshed. How can I commit my changes to that tool? Can somebody of the devteam grant me acces? Do I send the diff by email :-) ? Cheers, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 07/24/2013 11:17 AM, Peter Cock wrote: On Wed, Jul 24, 2013 at 9:40 AM, Joachim Jacob | VIB | joachim.ja...@vib.be wrote: Hi all, A Cheetah question: when I enter ; as a value in a text box of a tool (stored in $exp), Cheetah prints this as X, and passed this string to the tool. How to disable this behaviour in Cheetah? I have tried to play with #filter directives, but to no avail. Thanks, Joachim That sounds like the Galaxy character sanitation making the change, things like pipes etc can have unexpected results in command lines. Have a look at the sanitizer tag for use in the tool's XML file. 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/
Re: [galaxy-dev] Disable cheetah filtering
Hi, Okay, normally I would have forked the galaxy-dist and do a pull request with my change. But the change I want to commit is in the tool 'add_value', which is in the toolshed. Seems like a safer approach to me to contribute to the toolshed. How can I commit my changes to that tool? Can somebody of the devteam grant me acces? Do I send the diff by email :-) ? Yes, please send the patch to the mailing list and/or the devteam (toolshed should have a contact button). Also try to fill a trello card :) Thanks! Bjoern Cheers, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 07/24/2013 11:17 AM, Peter Cock wrote: On Wed, Jul 24, 2013 at 9:40 AM, Joachim Jacob | VIB | joachim.ja...@vib.be wrote: Hi all, A Cheetah question: when I enter ; as a value in a text box of a tool (stored in $exp), Cheetah prints this as X, and passed this string to the tool. How to disable this behaviour in Cheetah? I have tried to play with #filter directives, but to no avail. Thanks, Joachim That sounds like the Galaxy character sanitation making the change, things like pipes etc can have unexpected results in command lines. Have a look at the sanitizer tag for use in the tool's XML file. 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/
Re: [galaxy-dev] Disable cheetah filtering
On Wed, Jul 24, 2013 at 11:25 AM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi, Okay, normally I would have forked the galaxy-dist and do a pull request with my change. But the change I want to commit is in the tool 'add_value', which is in the toolshed. Seems like a safer approach to me to contribute to the toolshed. How can I commit my changes to that tool? Can somebody of the devteam grant me acces? Do I send the diff by email :-) ? Yes, please send the patch to the mailing list and/or the devteam (toolshed should have a contact button). Also try to fill a trello card :) Thanks! Bjoern In general the upstream repository for a given tool will depend on the tool author's preferences. They may not even use a separate repository and work directly with the ToolShed in some cases. In other cases you might be able to contribute directly via a github pull request (planned for the NCBI BLAST+ tools), or a bitbucket pull request (the Galaxy team like bitbucket). The 'add_value' tool is under 'devteam' and it was original in the main Galaxy repository under BitBucket - I don't know where it lives now outside the tool shed: http://toolshed.g2.bx.psu.edu/view/devteam/add_value Regards, 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/
Re: [galaxy-dev] Disable cheetah filtering
Hmm, seems that collaborating on tools is kind of a burden... Three places to notify this small change you say? (trello, galaxy-dev and direct emailing to the authors.) I have opted for Trello, card #1013 Cheers, J Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 07/24/2013 12:45 PM, Peter Cock wrote: On Wed, Jul 24, 2013 at 11:25 AM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi, Okay, normally I would have forked the galaxy-dist and do a pull request with my change. But the change I want to commit is in the tool 'add_value', which is in the toolshed. Seems like a safer approach to me to contribute to the toolshed. How can I commit my changes to that tool? Can somebody of the devteam grant me acces? Do I send the diff by email :-) ? Yes, please send the patch to the mailing list and/or the devteam (toolshed should have a contact button). Also try to fill a trello card :) Thanks! Bjoern In general the upstream repository for a given tool will depend on the tool author's preferences. They may not even use a separate repository and work directly with the ToolShed in some cases. In other cases you might be able to contribute directly via a github pull request (planned for the NCBI BLAST+ tools), or a bitbucket pull request (the Galaxy team like bitbucket). The 'add_value' tool is under 'devteam' and it was original in the main Galaxy repository under BitBucket - I don't know where it lives now outside the tool shed: http://toolshed.g2.bx.psu.edu/view/devteam/add_value Regards, 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/
Re: [galaxy-dev] Disable cheetah filtering
On Wed, Jul 24, 2013 at 1:56 PM, Joachim Jacob | VIB | joachim.ja...@vib.be wrote: Hmm, seems that collaborating on tools is kind of a burden... Three places to notify this small change you say? (trello, galaxy-dev and direct emailing to the authors.) I have opted for Trello, card #1013 Cheers, https://trello.com/c/GVq8Vpsi/1013-bug-some-characters-not-permitted-in-add-column-tool Well in this case the tool authors are the Galaxy Developers, so you can email them directly, via the galaxy-dev list, or their issue tracker which is Trello. Ideally every tool's README file would include contact details... 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/
Re: [galaxy-dev] Test ToolShed repository_dependencies.xml processing
Peter, Thank you for reporting this issue, it has been fixed in 10253:27b458743a11, and the test tool shed has been updated to that revision. --Dave B. On 7/23/13 12:29:34.000, Peter Cock wrote: On Tue, Jul 23, 2013 at 5:20 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Gred, I'm trying to update this repository (initially just to switch my README file to reStructuredText as the current plain text is not being rendered nicely): http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss Uploading my new tar-ball failed: Internal Server Error Galaxy was unable to sucessfully complete your request URL: http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=8067bb858e9138ab ... Same again for http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename which uses the same repository_dependencies.xml file. 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] [galaxy-iuc] [patch] enabling rst rendered readme file in TS
Hi peter, I've made this change in 10254:e22f360cda13, so now only those readme files whose file anme ends in .rst will be rendered as such. Thanks! Greg Von kuster On Jul 23, 2013, at 12:24 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Fri, Jul 12, 2013 at 3:35 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Björn, This one has been applied in changeset 10219:a7edac403b6c, and all of your patches are now running on the test tool shed. Thanks very much, Greg Von Kuster Hi Greg Björn, I think supporting reStructuredText is a good idea, but should not be done automatically, consider: http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040 This README file is named with the extension *.txt and does not render nicely if treated as *.rst, things like System Message: ERROR and System Message: WARNING are shown to the user. I suggest that the ToolShed only render like this if the README file is using the *.rst extension, but otherwise default to plain text (e.g. no extension or *.txt files). 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/
Re: [galaxy-dev] workflow: default parameters
Hi James, thanks for the short reply. I have created a trello card. Here is the link https://trello.com/c/SRxD991Y/1012-workflow-default-parameters Feel free to vote. Best regards, Jens -Ursprüngliche Nachricht- Von: ja...@taylorlab.org [mailto:ja...@taylorlab.org] Im Auftrag von James Taylor Gesendet: Montag, 22. Juli 2013 19:28 An: Keilwagen, Jens Cc: galaxy-...@bx.psu.edu Betreff: Re: [galaxy-dev] workflow: default parameters Not currently possible, but it shouldn't be too difficult to make work. Please file a Trello card. On Tue, Jul 9, 2013 at 11:36 AM, Keilwagen, Jens jens.keilwa...@jki.bund.de wrote: when building workflows we can choose for each parameter whether to 'set at runtime' or to 'set in advance' (when creating or editing the workflow). We are looking for a possiblity to set a default value that is used (only) for the workflow, i.e., we like to specify a value that might be used by most users, but might be altered by expert users. This value might be different from the default value of the corresponding tool. So far, we did not find any possiblity. -- James Taylor, Assistant Professor, Biology/CS, Emory University ___ 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] [galaxy-iuc] [patch] enabling rst rendered readme file in TS
On Tue, Jul 23, 2013 at 5:24 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Fri, Jul 12, 2013 at 3:35 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Björn, This one has been applied in changeset 10219:a7edac403b6c, and all of your patches are now running on the test tool shed. Thanks very much, Greg Von Kuster Hi Greg Björn, I think supporting reStructuredText is a good idea, but should not be done automatically, consider: http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040 This README file is named with the extension *.txt and does not render nicely if treated as *.rst, things like System Message: ERROR and System Message: WARNING are shown to the user. I suggest that the ToolShed only render like this if the README file is using the *.rst extension, but otherwise default to plain text (e.g. no extension or *.txt files). Thanks, Peter Thanks Greg for doing that: https://bitbucket.org/galaxy/galaxy-central/commits/e22f360cda1363d0c93a86d64c17032e7507b296 Here's a follow-up patch to hopefully fix the rendering of these revisions where I have switched to an *.rst file but the filename isn't used: http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/a119cd123b2d http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/a119cd123b2d Thanks, Peter $ hg diff diff -r e22f360cda13 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py Wed Jul 24 10:34:21 2013 -0400 +++ b/lib/tool_shed/util/metadata_util.py Wed Jul 24 15:39:44 2013 +0100 @@ -990,6 +990,7 @@ valid_filenames.extend( map( lambda f: '%s.rst' % f, readme_files ) ) valid_filenames.extend( readme_files ) valid_filenames.append( '%s.txt' % repository_name ) +valid_filenames.append( '%s.rst' % repository_name ) return valid_filenames def get_relative_path_to_repository_file( root, name, relative_install_dir, work_dir, shed_config_dict, resetting_all_metadata_on_repository ): ___ 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] Bug report
What format are the files you are trying to process with MACS in? -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jul 23, 2013 at 3:05 PM, Jianxin Wang jianxin.w...@oicr.on.ca wrote: Hi Galaxy dev team, I'm trying to the you galaxy server to do NGS peak calling: Tools - NGS: Peak Calling - MACS Model-based Analysis of ChIP-Seq. However, the page won't allow me enter the input files: the drop-down selection box won't show anything when clicked. Same problem for the ChIP-Seq Control File selection box. Please take a look and email me back if problem is fixed. Jianxin Wang, PhD Computational Biologist jianxin.w...@oicr.on.ca Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel: 416-673-8569 www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. ___ 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] Cloudman - is it possible to still use depreciated AMIs ?
The cluster status log has the following: * 14:49:00 - Setting up SGE... * 14:49:09 - Postgres service prerequisites OK; starting the service * 14:49:10 - PostgreSQL daemon NOT running. * 14:49:10 - PostgreSQL daemon NOT running. * 14:50:11 - --- PROBLEM, running command '/bin/su - postgres -c /usr/lib/postgresql/8.4/bin/pg_ctl -w -D /mnt/galaxy/db -l /tmp/pgSQL.log -o\-p 5910\ start' returned code '1' and following stderr: '' * 14:50:18 - PostgreSQL daemon NOT running. * 14:50:18 - Hadoop service prerequisites OK; starting the service * 14:50:31 - PostgreSQL daemon NOT running. * 14:50:45 - PostgreSQL daemon NOT running. * 14:50:58 - Done adding Hadoop service; service running. * 14:50:58 - PostgreSQL daemon NOT running. From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Ravpreet Setia [ravpreet.se...@oicr.on.ca] Sent: Tuesday, July 23, 2013 7:00 PM To: Dannon Baker Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Cloudman - is it possible to still use depreciated AMIs ? Hey, thanks for the response. The ssh issue was on my end and is now resolved. However, when I try the old AMI (ami-da58aab3), it mounts the new directory structure (meaning galaxyTools does not exist). Why does the old AMI have the directory structure of the new AMI? Along with that, PostgreSQL does not load properly, it is stuck at Starting up. I get the following error: FATAL: database files are incompatible with server DETAIL: The data directory was initialized by PostgreSQL version 9.1, which is not compatible with this version 8.4.7. From: Dannon Baker [dannon.ba...@gmail.com] Sent: Monday, July 22, 2013 5:01 PM To: Ravpreet Setia Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Cloudman - is it possible to still use depreciated AMIs ? Yes, you can still use the deprecated AMIs. What error are you seeing when you try to ssh in? On Mon, Jul 22, 2013 at 4:30 PM, Ravpreet Setia ravpreet.se...@oicr.on.camailto:ravpreet.se...@oicr.on.ca wrote: I tried launching an instance specifying ami-da58aab3 as the AMI but I am unable to SSH or access Cloudman using the instance's URL. ___ 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] job_conf.xml workers
Hi, what is the relationship between workers defined in universe and job_conf.xml? e.g.: [server:handler0] use = egg:Paste#http port = 9092 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 plugins workers=4 !-- workers is the number of threads for the runner's work queue. The default from plugins is used if not defined for a plugin. -- plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner/ plugin id=drmaa type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner workers=10/ /plugins a) do I have to specify the sum of the workers in job_conf.xml in universe? e.g. 4 local, 10 drmaa = 14 threadpool_workers per handler? Or is universe overridden by job_conf.xml? b) How many concurrent jobs can I then expect to have concurrently? 14 per handler? thank you very much, ido ___ 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] BWA Illumina Mapping / BWA Reference Genome
Hi Moritz I am not a galaxy tool shed expert, but I recommend you start with reading these wiki pages: http://wiki.galaxyproject.org/Tool%20Shed http://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy and then try installing BWA via the tool shed and ask (if any) specific questions (preferably with a new subject line) on the mailing list. Regards Hans-Rudolf On 07/22/2013 11:20 AM, Moritz Juchler wrote: Hey, with the tool file line I got it working :) Thanks a lot. Could you answer the question regarding Tool Shed: If I would use Tool Shed, could I skip all these manual steps? Is the installation of BWA with Tool Shed also this complicated or is it more simle? Best Moritz On 17 July 2013 09:51, Moritz Juchler juch...@stud.uni-heidelberg.de mailto:juch...@stud.uni-heidelberg.de wrote: Hey, no thats correct I did not use Tool Shed. If I would use it, could I skip all these manual steps? Is the installation of BWA with Tool Shed also this complicated or is it more simle? How did you not follow my steps :) I wrote down everything clearly, at least thats what I was hoping. And no I didnt write this line tool file=sr_mapping/bwa_wrapper.__xml / Thats the first time, I am seeing this tutorial :( I will try this out right now Best Moritz On 17 July 2013 09:42, Hans-Rudolf Hotz h...@fmi.ch mailto:h...@fmi.ch wrote: Hi Moritz I am struggling to follow what exactly you have done. As far as I can see, you did not use the toolshed (http://wiki.galaxyproject.__org/Tool%20Shed http://wiki.galaxyproject.org/Tool%20Shed) to install the BWA alinger tool, but did all manually? If so, have you added the following line: tool file=sr_mapping/bwa_wrapper.__xml / to the tool_conf.xml file, and restarted Galaxy? see also: http://wiki.galaxyproject.org/__Admin/Tools/Add%20Tool%__20Tutorial http://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial Hope this helps Hans-Rudolf On 07/16/2013 08:35 PM, Moritz Juchler wrote: Hello Ladies and Gentlemen, I am Moritz Juchler from University Heidelberg. For my Bachelor thesis I have to choose a bioinformatic pipeline management tool to find SNP's in genomes from hcc patients. My decision was made in favor of galaxy. I have a 64-bit openSuse 11.3 server. I have installed Galaxy locally, since we have a) very large files (30GB per patient) and b) the data is protection sensitive. I kept close to http://wiki.galaxyproject.org/__Admin/Get%20Galaxy http://wiki.galaxyproject.org/Admin/Get%20Galaxy Now I would like to run this bpipe pipeline: http://pastebin.com/sZd5vfdL And the first step is to align my genome to a _hg19 reference genome_ which I have locally under /genedata/human_genome_GRCh37/__. trr@portalmoritz:~ ls -l /genedata/human_genome_GRCh37/ total 8486312 -rw-r--r-- 1 trr root 3199905909 2013-06-25 16:44 hg19.fa -rw-r--r-- 1 trr root 8591 2013-07-01 16:06 hg19.fa.amb -rw-r--r-- 1 trr root 4040 2013-07-01 16:06 hg19.fa.ann -rw-r--r-- 1 trr root 3137161344 2013-07-01 16:05 hg19.fa.bwt -rw-r--r-- 1 trr root 784290318 2013-07-01 16:06 hg19.fa.pac -rw-r--r-- 1 trr root 1568580688 2013-07-01 16:31 hg19.fa.sa http://hg19.fa.sa http://hg19.fa.sa _bwa is installed and gives me:_ trr@portalmoritz:~ bwa Program: bwa (alignment via Burrows-Wheeler transformation) Version: 0.7.5a-r405 Contact: Heng Li l...@sanger.ac.uk mailto:l...@sanger.ac.uk mailto:l...@sanger.ac.uk mailto:l...@sanger.ac.uk Then I tried to follow this guide: http://wiki.galaxyproject.org/__Admin/NGS%20Local%20Setup http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup to get the reference files and http://wiki.galaxyproject.org/__Admin/Config/Tool%__20Dependencies http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies. This is my _$PATH_ trr@portalmoritz:~ echo $PATH /home/trr/bin:/usr/local/bin:/__usr/bin:/bin:/usr/bin/X11:/__usr/X11R6/bin:/usr/games:/__home/trr/bpipe-0.9.8/bin:/__home/trr/bwa-0.7.5a:/home/trr/__samtools-0.1.19 _In the universe_wsgi.ini I changed:_ tool_dependency_dir = /home/trr/galaxy-dist/tool___dependency_dir debug =
Re: [galaxy-dev] job_conf.xml workers
use_threadpool and threadpool_workers specify the number of threads for handling web requests and have nothing to do with job running. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Wed, Jul 24, 2013 at 11:02 AM, Ido Tamir ta...@imp.ac.at wrote: Hi, what is the relationship between workers defined in universe and job_conf.xml? e.g.: [server:handler0] use = egg:Paste#http port = 9092 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 plugins workers=4 !-- workers is the number of threads for the runner's work queue. The default from plugins is used if not defined for a plugin. -- plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner/ plugin id=drmaa type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner workers=10/ /plugins a) do I have to specify the sum of the workers in job_conf.xml in universe? e.g. 4 local, 10 drmaa = 14 threadpool_workers per handler? Or is universe overridden by job_conf.xml? b) How many concurrent jobs can I then expect to have concurrently? 14 per handler? thank you very much, ido ___ 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] job_conf.xml workers
Ah yes, this was local_job_queue_workers and cluster_job_queue_workers in universe.ini thank you very much, ido On Jul 24, 2013, at 5:10 PM, James Taylor ja...@jamestaylor.org wrote: use_threadpool and threadpool_workers specify the number of threads for handling web requests and have nothing to do with job running. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Wed, Jul 24, 2013 at 11:02 AM, Ido Tamir ta...@imp.ac.at wrote: Hi, what is the relationship between workers defined in universe and job_conf.xml? e.g.: [server:handler0] use = egg:Paste#http port = 9092 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 plugins workers=4 !-- workers is the number of threads for the runner's work queue. The default from plugins is used if not defined for a plugin. -- plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner/ plugin id=drmaa type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner workers=10/ /plugins a) do I have to specify the sum of the workers in job_conf.xml in universe? e.g. 4 local, 10 drmaa = 14 threadpool_workers per handler? Or is universe overridden by job_conf.xml? b) How many concurrent jobs can I then expect to have concurrently? 14 per handler? thank you very much, ido ___ 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] HTML output with external Javascript
Hi Gromobir, The file that Gift is producing is already an html file and there's already an html datatype in Galaxy by default. The output file in question just invokes remote javascript libraries inside script tags, and this seems to be tripping up Galaxy's data viewer. We've tried turning off the the html sanitizer, as mentioned below, but this doesn't seem to have any effect. We've tried downloading and referencing the javascript libraries in /static/js as well. I know that the new visualization platform in Galaxy uses a lot of external javascript libraries like D3Š does anyone know how that is being handled differently? Thanks, Andrew -- Andrew Stewart Office of Research Information Services (ORIS), Office of the Chief Information Officer (OCIO), Smithsonian Institution 202-633-2840 On 7/23/13 12:00 PM, galaxy-dev-requ...@lists.bx.psu.edu galaxy-dev-requ...@lists.bx.psu.edu wrote: On 07/23/2013 05:14 PM, Sinthong, Phanwadee wrote: Hi galaxy-dev, I have a tool that generates a HTML output file which uses some javascript library. I cannot view the output file with the eye button in Galaxy, but it still works fine from the HTML file opened out of the file directory. I changed the sanitize_all_html = False and restarted the galaxy server as some earlier post suggested but still couldn't view the output file. What else can I do to execute Javascript in the Galaxy browser? Which library are you trying to use? You may have to define your own datatype and add something like the following to the file datatypes_conf.xmlafterwards: datatype extension=html type=galaxay.datatypes.xml:Html mimetype=application/html ___ 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] All processes are freezed
The best contact address for these kinds of issues is galaxy-b...@bx.psu.edu . There was a brief delay with some jobs running, but everything should be working fine now. -Dannon On Wed, Jul 24, 2013 at 5:30 AM, Ali Sharifi Zarchi ashari...@gmail.comwrote: Hi everybody Since yesterday all processes I have run on Galaxy main are waiting. The system displayed a message to contact a Galaxy admin, but I could find no other way rather than this mailing list. Is this freeze due to a public maintenance, or it's just my problem? Best wishes, Ali ___ 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] uninstalling migrated tool
Shantanu, I've yet been unable to reproduce this issue on a local installation of a tool shed. If I do manage to reproduce it, I will re-open the issue and find a fix. --Dave B. On 7/17/13 16:31:56.000, Greg Von Kuster wrote: Hello Shantanu, I've created a Trello card for this - we'll take a look as soon as possible. https://trello.com/c/1hXOJPlZ/994-toolshed-from-shantanu-pavgi-on-7-12-13-it-seems-like-if-we-uninstall-a-migrated-tool-then-it-s-entry-in-the-migrated-tools-conf Thanks, Greg Von Kuster On Jul 12, 2013, at 12:42 PM, Shantanu Pavgi (Campus) pa...@uab.edu wrote: It seems like if we uninstall a migrated tool then it's entry in the migrated_tools_conf.xml file doesn't get deleted. Does it need to be removed manually? -- Thanks, Shantanu ___ 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] Bowtie2 error: Creates a 62 kb file.
[Copying the list]. -Original Message- From: Maddhi, Srinivas Maddhi srinivas-mad...@uiowa.edu Date: Wednesday, July 24, 2013 10:01 AM To: Perez, Ricardo ricky_...@neo.tamu.edu Subject: Re: [galaxy-dev] Bowtie2 error: Creates a 62 kb file. Hi Ricardo, Ensuring that the appropriate reference indices are present, properly configured and selected when running bowtie2 might help address this problem. -Original Message- From: Perez, Ricardo ricky_...@neo.tamu.edu Date: Wednesday, July 24, 2013 1:35 AM To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Bowtie2 error: Creates a 62 kb file. Dear all, Today we ran some problems when running bowtie2. When we run bowtie2, the run manages to complete. However, bowtie2 creates a 62kb file. The error log that we get is the following: galaxy.jobs DEBUG 2013-07-23 17:09:42,378 (1483) Persisting job destination (destination id: local:///) galaxy.jobs.handler INFO 2013-07-23 17:09:42,392 (1483) Job dispatched galaxy.tools DEBUG 2013-07-23 17:09:42,556 Building dependency shell command for dependency 'bowtie2' galaxy.tools WARNING 2013-07-23 17:09:42,556 Failed to resolve dependency on 'bowtie2', ignoring galaxy.tools DEBUG 2013-07-23 17:09:42,556 Building dependency shell command for dependency 'samtools' galaxy.tools WARNING 2013-07-23 17:09:42,556 Failed to resolve dependency on 'samtools', ignoring galaxy.jobs.runners.local DEBUG 2013-07-23 17:09:42,626 (1483) executing: bowtie2 --version /usr/local/galaxy/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_1483; python /usr/local/galaxy/galaxy-dist/tools/sr_mapping/bowtie2_wrapper.py --num-threads=4 --output=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1673.da t --indexes-path=/data/db/fungidb/Ncrassa_OR74A/bowtie2/Ncrassa_wt_Chr01.C h r07.+ChrM.+rDNA_v12 --single-paired=paired --input1=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1668.da t --input2=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1669.da t -I 0 -X 250 --settings=preSet galaxy.jobs DEBUG 2013-07-23 17:09:42,696 (1483) Persisting job destination (destination id: local:///) galaxy.jobs.runners.local DEBUG 2013-07-23 17:09:42,766 execution finished: bowtie2 --version /usr/local/galaxy/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_1483; python /usr/local/galaxy/galaxy-dist/tools/sr_mapping/bowtie2_wrapper.py --num-threads=4 --output=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1673.da t --indexes-path=/data/db/fungidb/Ncrassa_OR74A/bowtie2/Ncrassa_wt_Chr01.C h r07.+ChrM.+rDNA_v12 --single-paired=paired --input1=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1668.da t --input2=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1669.da t -I 0 -X 250 --settings=preSet galaxy.jobs.runners DEBUG 2013-07-23 17:09:42,850 executing external set_meta script for job 1483: /usr/local/galaxy/galaxy-dist/set_metadata.sh ./database/files /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483 . /usr/local/galaxy/galaxy-dist/universe_wsgi.ini /usr/local/galaxy/galaxy-dist/database/tmp/tmpUiqpPD /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/gal a xy.json /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/met a data_in_HistoryDatasetAssociation_1767_wqhEmr,/usr/local/galaxy/galaxy-di s t/database/job_working_directory/001/1483/metadata_kwds_HistoryDatasetAss o ciation_1767_qVZjpG,/usr/local/galaxy/galaxy-dist/database/job_working_di r ectory/001/1483/metadata_out_HistoryDatasetAssociation_1767_vIfpRO,/usr/l o cal/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_r e sults_HistoryDatasetAssociation_1767_UNl6OR,,/usr/local/galaxy/galaxy-dis t /database/job_working_directory/001/1483/metadata_over! ride_HistoryDatasetAssociation_1767_MZilrL 165.91.11.135 - - [23/Jul/2013:17:09:43 -0500] GET /api/histories/ca8efa3c47500414 HTTP/1.1 200 - http://galaxy.tamu.edu/history; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.22 (KHTML, like Gecko) Ubuntu Chromium/25.0.1364.160 Chrome/25.0.1364.160 Safari/537.22 165.91.11.231 - - [23/Jul/2013:17:09:43 -0500] GET /history HTTP/1.1 200 - http://galaxy.tamu.edu/tool_runner/index; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.71 Safari/537.36 165.91.11.231 - - [23/Jul/2013:17:09:43 -0500] GET /api/histories/1ab12f1e464820dd HTTP/1.1 200 - http://galaxy.tamu.edu/history; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.71 Safari/537.36 165.91.11.231 - - [23/Jul/2013:17:09:43 -0500] GET /history/get_display_application_links HTTP/1.1 200 - http://galaxy.tamu.edu/history; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/537.36 (KHTML, like Gecko)
Re: [galaxy-dev] tool input is folder rather than file
You'll want to use composite datatypes: http://wiki.galaxyproject.org/Admin/Datatypes/Composite%20Datatypes On Jul 24, 2013, at 3:08 AM, Pankaj Narang wrote: Dear Developers, I want to design a tool whose input is folder containing files and sub-folders. I was wandering which value should I assign to TYPE attribute of PARAM tag in INPUTS. -- Best regards, Pankaj Narang ___ 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] CloudMan Error
Hi- there is a new problem: started 07/24/2013 21:16:27 ./test_dependencies.sh All required executables found in PATH All required R packages are installed Required module not found: /mnt/galaxyData/custom/bin/python_libs/lib/python/pysam-0.6-py2.7-linux-x86_64.egg/csamtools.so: undefined symbol: PyCapsule_New Error in ./test_dependencies.sh: 256 at msg/Utils.pm line 25. On Mon, Jul 22, 2013 at 5:04 PM, Dannon Baker dannon.ba...@gmail.comwrote: The warning message printed by the first ssh attempt indicates that you have no cloudman_key_pair.pem in the directory you executed the ssh command from. Find this file (or create a new one) and you'll be able to ssh. Good luck, and please keep threads on the list instead of emailing directly. Thanks! -Dannon On Mon, Jul 22, 2013 at 1:36 PM, deniz...@gmail.com wrote: Hi- the share string appears to be loading, but I am unable to ssh into my instance using the provided command, or anything like it. Instead I get the following: denizerezyilmaz$ ssh -i cloudman_key_pair.pem ubu...@ec2-54-242-61-164.compute-1.amazonaws.com Warning: Identity file cloudman_key_pair.pem not accessible: No such file or directory. OR: denizerezyilmaz$ ssh ec2-54-242-61-164.compute-1.amazonaws.com Permission denied (publickey). What am I missing? Thank you, Deniz ___ 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] Lumi wrapper for Galaxy
Hello group, I am trying to write lumi wrapper for Galaxy. Is anyone is writing or already have written lumi wrapper for Galaxy. I couldn't find in both galaxy main tool shed and test tool shed. Regards Sachit ___ 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/
