October 2008 - galaxy-user - lists.galaxyproject.org

Running development and live servers side-by-side
by Chris Cole 17 Nov '08

17 Nov '08

What is the best way to work with development and live versions of Galaxy concurrently and being able to have access to the same data (e.g. user histories)? Currently, I'm trying to run two instances of galaxy at the same time using the same MySQL database back-end and pointing to the same user files (via softlinks). Does this way madness lie? Although, it does seem to be working... I'm asking this because if we do go down the route of deploying Galaxy here, we'd like to be able to be able to test new tools without constantly having to restart the server and annoy the users. Cheers, Chris

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Galaxy and Arabidopsis
by Vesselin Baev 05 Nov '08

05 Nov '08

Dear All, Is it possible (and how) for Galaxy to work with Arabidopsis genome? Vesko -- ------------------------------------------------ Dr. Vesselin Baev Research Assistant Professor University of Plovdiv Dept. Molecular Biology Bioinformatics Group Tzar Assen 24 Plovdiv 4000, BULGARIA +359 32 261 (560) +359 89 43 80 945 Skype: vebaev vebaev(a)gmail.com baev(a)uni-plovdiv.bg http://plantgene.eu/

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SecurityFeatures - admin_users
by Andrew Olson 05 Nov '08

05 Nov '08

I'd like to set up admin_users on my galaxy installation. Adding this to universe_wsgi.ini has no effect. What do I need to do to get this working? Andrew

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Using SGE cluster
by Henrikki Almusa 31 Oct '08

31 Oct '08

Hi, I'm trying to get SGE cluster to run some tools on galaxy. I've set the 'start_job_runners = sge' and 'default_cluster_job_runner = local:///'. I'm hoping that this setup would run tools locally, unless tool is set to run on cluster in '[galaxy:tool_runners]' section. However this seems to fail with following message: Exception: SGEJobRunner requires DRMAA_python which was not found The DRMAA python package however is installed as is libdrmaa.so.1.0. And importing the DRMAA package works in python command prompt. How should I proceed with this? Regards, -- Henrikki Almusa

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set an upload size limit
by Davide Cittaro 30 Oct '08

30 Oct '08

Hi all, how can I set a size limit for data to be uploaded in galaxy? Thanks d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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About adding tools
by Henrikki Almusa 30 Oct '08

30 Oct '08

Hi, I'm looking at how to add tools to galaxy. Is there any info on what the tool.xml can have within it (dtd or documentation or something)? Another thing is the command line. Is it possible to use optional command line switches that don't have values. Eg. grep has option '-i' which means ingore case (and if not given it is case sensitive). Regards, -- Henrikki Almusa

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passing SGE parameters
by Chris Cole 29 Oct '08

29 Oct '08

Hi, Is it possible to specify SGE parameters on a job-by-job basis? For example, say I want set off an array job or specify a parallel environment for certain jobs. Thanks, Chris

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Tabular output column headings
by Andrew Olson 29 Oct '08

29 Oct '08

I have a tool that generates tabular output but I don't know how to get the column headings assigned. The output format is not fixed since the user decides what data goes into the output. Andrew Olson

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Simplejson reimport error
by Sean Davis 29 Oct '08

29 Oct '08

/home/www/galaxy/lib/galaxy/eggs/__init__.py:529: UserWarning: Module simplejson was already imported from /usr/local/lib64/python2.5/site-packages/simplejson-1.7.1-py2.5.egg/simplejson/__init__.py, but /home/www/galaxy/eggs/py2.5-noplatform/simplejson-1.5-py2.5.egg is being added to sys.path pkg_resources.working_set.require( "%s==%s" % ( name, egg.get_vertag() ) ) I got this when doing Get Data->UCSC table browser->get BED of ucsc known genes; the download failed. It looks like there are some version confusions here. Any suggestions? Sean

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Multiple outputs
by Andrew Olson 29 Oct '08

29 Oct '08

I have a tool that uses the <repeat> tag in the xml file to gather an arbitrary number of inputs from the history. The tool gathers all the inputs and modifies some of them. Is it possible to create a new output for each of the corresponding inputs? Would it be defined in the tool.xml or can the <command> that is run let Galaxy know about the new outputs somehow? Andrew Olson

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