- galaxy-dev - lists.galaxyproject.org

tool with no inputs?
by Kostas Karasavvas 06 Dec '10

06 Dec '10

Hi all, Is that possible? As long as there is no <inputs> tag or if there is an empty inputs tag I get an error. When I provide an input it works. Is there a way around it? I need it to access a server that could take zero arguments. Cheers, Kostas

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2011 GMOD Spring Training, March 8-12
by Dave Clements, GMOD Help Desk 03 Dec '10

03 Dec '10

Applications are now being accepted for the 2011 GMOD Spring Training course a five-day hands-on school aimed at teaching new GMOD administrators how to install, configure and integrate popular GMOD components. The course will be held March 8-12 at the US National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, as part of GMOD Americas 2011. Links: * http://gmod.org/wiki/2011_GMOD_Spring_Training * http://gmod.org/wiki/GMOD_Americas_2011 * http://www.nescent.org/ These components will be covered: * Apollo - genome annotation editor * Chado - biological database schema * Galaxy - workflow system * GBrowse - genome viewer * GBrowse_syn - synteny viewer * GFF3 - genome annotation file format and tools * InterMine - biological data mining system * JBrowse - next generation genome browser * MAKER - genome annotation pipeline * Tripal - web front end to Chado databases The deadline for applying is the end of Friday, January 7, 2011. Admission is competitive and is based on the strength of the application, especially the statement of interest. The 2010 school had over 60 applicants for the 25 slots. Any application received after deadline will be automatically placed on the waiting list. The course requires some knowledge of Linux as a prerequisite. The registration fee will be $265 (only $53 per day!). There will be a limited number of scholarships available. This may be the only GMOD School offered in 2011. If you are interested, you are strongly encouraged to apply by January 7. Thanks, Dave Clements -- http://gmod.org/wiki/GMOD_Americas_2011 http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/Help_Desk_Feedback

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Loading new tools without restarting galaxy
by Chaolin Zhang 03 Dec '10

03 Dec '10

Hi, We have a local galaxy mirror installed and running. Is there a way to add new tools without restarting galaxy? Thanks! Chaolin

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pbs pro and galaxy (change status error)
by Laure QUINTRIC 02 Dec '10

02 Dec '10

Hello, We almost succeed in using drmaa-0.4b3 with galaxy and pbs pro : The job launched from galaxy runs on our cluster but when job status changes to finished, there's an error in drmaa python egg. Here is the server log : galaxy.jobs.runners.drmaa ERROR 2010-11-26 17:11:10,857 (21/516559.service0.ice.ifremer.fr) Unable to check job status Traceback (most recent call last): File "/home12/caparmor/bioinfo/galaxy_dist/lib/galaxy/jobs/runners/drmaa.py", line 252, in check_watched_items state = self.ds.jobStatus( job_id ) File "/usr/lib/python2.5/site-packages/drmaa-0.4b3-py2.5.egg/drmaa/__init__.py", line 522, in jobStatus File "/usr/lib/python2.5/site-packages/drmaa-0.4b3-py2.5.egg/drmaa/helpers.py", line 213, in c return f(*(args + (error_buffer, sizeof(error_buffer)))) File "/usr/lib/python2.5/site-packages/drmaa-0.4b3-py2.5.egg/drmaa/errors.py", line 90, in error_check raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value)) InternalException: code 1: pbs_statjob: Job %s has finished galaxy.jobs.runners.drmaa WARNING 2010-11-26 17:11:10,861 (21/516559.service0.ice.ifremer.fr) job will now be errored galaxy.jobs.runners.drmaa DEBUG 2010-11-26 17:11:10,986 (21/516559.service0.ice.ifremer.fr) User killed running job, but error encountered removing from DRM queue: code 1: pbs_deljob: Job %s has finished Any idea ? Thanks a lot Laure

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Independent Assessment of Galaxy
by Anton Nekrutenko 02 Dec '10

02 Dec '10

Dear galaxy-dev members: Professor Nils Christophersen (Department of Informatics, University of Oslo) has asked me to provide him with a few contacts of people who are independent from the core galaxy team. He needs these to get an idea why people have chosen Galaxy for their particular needs. If some of you would be willing to send him (he is CC'ed on this e-mail) a short blurb we would very much appreciate this! Thanks for your time! anton Anton Nekrutenko http://usegalaxy.org

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why is my lastz process showing it is not finished?
by David Hoover 02 Dec '10

02 Dec '10

I've set up a local instance of Galaxy, and have submitted a lastz job on some fake data. It ran for about 3 minutes and then finished, as shown in the logfiles and by system tools like top and ps. However, the web page shows the spinning wheel and yellow box for 10 minutes until the box turned green and wheel stopped spinning. Why is there such a delay between when the job completes and when the web page shows it is finished? Is there a configuration element I'm missing? David Hoover Helix Systems Staff http://helix.nih.gov

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Galaxy runs maximum 2 jobs in parallel even though local_job_queue_workers is set to 7
by Nicolas Delhomme 02 Dec '10

02 Dec '10

Hi all, Since I "pulled" 4640:8729d2e29b02 (Nov 17th), my local installation of Galaxy only runs 2 jobs at a time, even though more could be run and the "local_job_queue_workers" is set to 7 in the universe_wsgi.ini. I didn't see anything in the email archive, nor on the wiki concerning this. Did I miss it? If not, what could be the problem? Thx, Nico --------------------------------------------------------------- Nicolas Delhomme High Throughput Functional Genomics Center European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delhomme(a)embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany ---------------------------------------------------------------

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lastz_seqs data table; error preparing job
by Glen Beane 01 Dec '10

01 Dec '10

I just updated my local Galaxy install to the latest galaxy-dist. The lastz tool seems to have been changed so it needs a lastz_seqs data table. I added (as a guess) <table name="lastz_seqs"> <columns>name, value</columns> <file path="tool-data/lastz_seqs.loc" /> </table> to tool_data_table_conf.xml. the lastz tool will now load, and it shows my reference sequences in the drop down list. However, now when I run lastz I get an error while it is trying to setup the job: Traceback (most recent call last): File "/galaxydata/galaxy-setup/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 186, in queue_job job_wrapper.prepare() File "/galaxydata/galaxy-setup/galaxy-dist/lib/galaxy/jobs/__init__.py", line 368, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/galaxydata/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 1524, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/galaxydata/galaxy-setup/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/galaxydata/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 119, in respond IndexError: list index out of range -- Glen L. Beane Software Engineer The Jackson Laboratory Phone (207) 288-6153

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building NGS indexes on user sequences
by Michael Pheasant 01 Dec '10

01 Dec '10

Hi We want to allow users to index sequences in galaxy (for example in the data libraries) for use with NGS tools (Bowtie, BWA, etc). Has anyone made tools for NGS indexing? It will also require changing the .loc files for the NGS tools & dynamic re-configuring of tools, which is all possible. Users might want to index & map reads to either their own sequences or other sequences that arent available in the default list, and this would remove the need for admin intervention. Any one else doing something similar? Or can it be done now & I just dont see it? Cheers, Mike.

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cleaning old data set
by Vipin TS 01 Dec '10

01 Dec '10

Dear Galaxy team, With reference to the document sited at http://bitbucket.org/galaxy/galaxy-central/wiki/Config/PurgeHistoriesAndDat…, I tried to clean up old dataset from our Galaxy instance. For example: deleting the userless histories based on the time span, the clean up scripts run perfectly but the dataset is not removed from the disk. Thanks for your support, Vipin T S Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany Tel:+49 7071 601 824

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