April 2014 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] [galaxy-bugs] Galaxy modules deployment
by Martin Čech 03 Apr '14

03 Apr '14

Hello, it is great you want to share tools with others through Galaxy, thank you! We call added software a 'Galaxy tool'. You can start by reading the tool basics in this page: https://wiki.galaxyproject.org/Admin/Tools and then you can browse through wiki where the vast of information about tool creation is available through tutorials. What you want is to 'wrap' your software for use within Galaxy with an XML file (sometimes called 'tool definition file' or 'wrapper') that will define the interactions of Galaxy and your software and the user interface of the tool page in Galaxy. You develop the tool first on your local Galaxy and then after it is working there you can submit your tool to the Tool Shed (Galaxy's appstore - https://wiki.galaxyproject.org/ToolShed) After your tool is in the Tool Shed it can be installed by any Galaxy worldwide. If you have any questions just ask in the dev-list mailing list (CCed in this conversation). Martin, Galaxy team On Thu, Apr 3, 2014 at 12:36 AM, <uthay(a)bioinfo.sastra.edu> wrote: > Dear Sir/Mam, > > As a part of our project work, we have developed some Bioinformatics > modules such as finding interactions for protein, displaying the contacts. > We are interested in deploying our modules in your Galaxy platform. Is that > possible? If so, what is the procedure? Can you guide us? > > Regards, > M. Udayakumar, > Dept. of Bioinformatics, > SASTRA University, > Thanjavur,Tamil Nadu, INDIA. > > >

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exported Workflows can contain full-path information
by Björn Grüning 03 Apr '14

03 Apr '14

Hi, if you export workflows it can happen that your *.ga file contains full-path informations to the chromosome len file. For example try to export the "mergeCols1" or the "trimmer" tool. The field chromInfo will have a full path attached. I don't think that will cause any harm, but it would be nice to omit this information. Trello Card is here: https://trello.com/c/TNUvq8X3 Ciao, Bjoern

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restarting multiple web workers
by Langhorst, Brad 03 Apr '14

03 Apr '14

Hi, I’m using the multiple web server stuff described here: https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling that seems to address the responsiveness issues i see when many users are active. However, when i add a new tool - it does not alway show up (only for one of the workers maybe?) Right now I’m restarting, but this costs a minute or two of downtime as the server starts up. Has anyone experimented with rolling restarts of web server processes? Alternatively, has anyone found a good way to speed up the startup process? Thanks! Brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist

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Select Random Lines - Not Working
by Unmesh Jadhav 03 Apr '14

03 Apr '14

Hello, I am trying to Select Random Lines (10million out of 39 million in a bed file) using the Galaxy tool and the tool is not responding for more than almost 12 hrs now. I have used this tool before for similar jobs and it has performed really well and fast. I would really appreciate if you could suggest how we handle this. Thank you, Unmesh

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ENA SRA data retrieval with Cloudman
by Mohammad Heydarian 03 Apr '14

03 Apr '14

Hi Cloudman Development Team, I noticed on the most recent Cloudman release (revision 11219:5c789ab4144a<http://bitbucket.org/galaxy/galaxy-dist/changesets/5c789ab4144a>) that there is no option to "Get Data" from the ENA SRA. We've found that retrieving large (fastq) data sets from public databases into Galaxy/Cloudman is the most convenient from the ENA SRA option in the "Get Data" menu. Will this option be coming back, or is the ENA SRA option permanently removed? Cheers, Mo Heydarian

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label element
by Jun Fan 03 Apr '14

03 Apr '14

Hi all, It seems that the recent release does not support label element anymore, i.e. no sub-section with the section title displayed in grey. Is there any alternative way to organize the tool under one big section? Best regards! Jun

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Problems submitting using PBS Pro 12.1
by Luca Toldo 02 Apr '14

02 Apr '14

Dear all, SUSE SLE 11 SP 1, with PBS Pro 12.1 client delivers galaxy.jobs.runners ERROR 2014-04-02 18:28:43,740 (249) Unhandled exception calling queue_job Traceback (most recent call last): File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 62, in run_next method(arg) File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 151, in queue_job external_job_id = self.ds.runJob(jt) File "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py", line 331, in runJob _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate) File "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/helpers.py", line 213, in c return f(*(args + (error_buffer, sizeof(error_buffer)))) File "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py", line 90, in error_check raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value)) InvalidAttributeValueException: code 14: Illegal attribute or resource value: Illegal attribute or resource value If I do qsub -q NGSq /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/249/galaxy_249.sh however the qsub returns 12345.myserver and the corresponding qstat | grep -i galaxy 12345.myserver galaxy_249.sh galaxy 00:00:00 E NGSq Is the above error message perhaps related with a) PBS 12.1 b) drmaa-0.7-py2.6.egg I am trying to compile pbs-drmaa-1.0.17 but there are problems ... any advice ? any alternative ? Thanks luca

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snpEff and FASTQ Summary Statistics errors
by Wang, Xiaofei 02 Apr '14

02 Apr '14

Dear there, When I used SnpEff in local galaxy instance, I got an error: Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j Also, when I used the FASTQ Summary Statistics, I got an error like this: Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/... I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!

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Problem with executing newly installed tools (via admin)
by Nicolas Cybulski 02 Apr '14

02 Apr '14

Hi, I have installed the Picard tools using the Tool-shed functionality in the admin tools. The tools and requisites have been correctly installed and run correctly. The insert statement to the event table fails however. I get the following error on screen: |OperationalError: (OperationalError) (1241, 'Operand should contain 1 column(s)') 'INSERT INTO event (create_time, update_time, history_id, user_id, message, session_id, tool_id) VALUES (%s, %s, %s, %s, %s, %s, %s)' (datetime.datetime(2014, 4, 2, 9, 32, 47, 823142), datetime.datetime(2014, 4, 2, 9, 32, 47, 823170), 35L, 4L, "Tool params: {'histWidth': u'0', 'deviations': u'10.0', 'malevel': u'ALL_READS', 'input_file': u'5266', 'out_prefix': u'Insertion size metrics', 'refresh': u'refresh', 'minPct': u'0.05', 'tool_state': u'800254cf010000316164663833323133363237333739303833323639353065346362343762393730383966363664313a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u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0', u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0']) |The problem seems to be a duplicate entry of the tool_id |[u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0', u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0'] |In the shed_tool_conf.xml the tools are generated as follows <tool file="toolshed.g2.bx.psu.edu/repos/devteam/picard/ab1f60c26526/picard/rgPicardIns…" guid="toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0"> If I change this guid to something less complicated like <tool file="toolshed.g2.bx.psu.edu/repos/devteam/picard/ab1f60c26526/picard/rgPicardIns…" guid="testPicard"> and restart galaxy it works ... for all tools (so not only the one that I've changed). Does anyone have an idea as to why this is ? kind regards, Nicolas

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Bowtie2 and tophat2 data library set up
by Huayan Gao 01 Apr '14

01 Apr '14

Hi, I wanted to use bowtie2 and tophat2 locally. I remembered you have instructions about how to set up the library here, but it is not accessible any more. https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Can you direct me to the right page or send me the documents please? Thanks, Huayan

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