December 2010 - galaxy-dev - lists.galaxyproject.org

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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