September 2011 - galaxy-dev - lists.galaxyproject.org

Galaxy API question: workflow_execute
by Roxanne Tapia 06 Sep '11

06 Sep '11

I was trying to use the workflow_execute.py And I can't understand the last argument: usage: workflow_execute.py key url workflow_id history step=src=dataset_id So in step=src=dataset_id step: I think equals the next step #in the history? src: ??? dataset_id: This has to be the dataset id from a data library which I can get by using display.py to query libraries & contents of libraries. Right? Can anyone explain this to me? Roxanne Tapia Software Developer 3 B-6, Genome Science Bioscience Division rox(a)lanl.gov (505)665-0206

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mycoplasma genomes - suggestion
by Lukasz Kielpinski 06 Sep '11

06 Sep '11

Hello everybody, I would like to suggest including mycoplasma genomes (preferably all genomes in one file) as reference genomes. It would enable fast checking if cells used for deep-seq experiments were not contaminated. Best, Lukasz

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Galaxy API question - histories
by Roxanne Tapia 06 Sep '11

06 Sep '11

Is there a way to create/view histories via the api, and to associate data in libraries to histories? Then to share the histories or make them public, and build a URL to view the history? Roxanne Tapia Software Developer 3 B-6, Genome Science Bioscience Division rox(a)lanl.gov (505)665-0206

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Galaxy API question:
by Roxanne Tapia 06 Sep '11

06 Sep '11

Hi, I was going through the examples in the README, and everything went along fine until I tried to upload files from the import directory: usage: library_upload_from_import_dir.py key url folder_id file_type server_dir dbkey I don't understand what the last two arguments 'server_dir' and 'dbkey' represent, or how to determine the correct values to pass along. I can, however, successfully upload via the import dir from the webapp. Any help would be appreciated, Roxanne Tapia Software Developer 3 B-6, Genome Science Bioscience Division LANL

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Quotas
by SHAUN WEBB 06 Sep '11

06 Sep '11

Hi. I am interested in putting quotas in to effect on our local Galaxy server. From the admin page I can create a quota but this only seems to apply to disk space. I noticed on your test site you have quotas for concurrent jobs also. Have I missed how to set this or is this functionality not available in galaxy-dist yet? 2 other issues: 1) My account says I am using "0 bytes" in the top right corner although my history displays 456mb of data? 2) Are quotas set by default? I was able to create quotas before I had updated universe_wsgi.ini to include enable_quotas = True Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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(no subject)
by Kristen Eisenberg 06 Sep '11

06 Sep '11

[galaxy-dev] Failure to prepare job error Hello, I'm running a Python/R tool from my Amazon Galaxy instance. To use R, I import a package I've installed called PypeR. My tool works fine from the command line, but when I try to run it on my Amazon instance, it gives me this error: Traceback (most recent call last): File "/nfs/software/galaxy/lib/galaxy/jobs/runners/local.py", line 61, in run_job job_wrapper.prepare() File "/nfs/software/galaxy/lib/galaxy/jobs/__init__.py", line 371, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/nfs/software/galaxy/lib/galaxy/tools/__init__.py", line 1543, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/nfs/software/galaxy/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/nfs/software/galaxy/eggs/Cheetah-2.2.2-py2.6-linux-i686-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1311891781_86_41894.py", line 83, in respond EOFError: EOF when reading a line With the additional caption "failure to prepare job". I've been struggling with this for days, and I'm pretty sure I don't have a typo in my .xml file. How can I solve this? Kristen Eisenberg Billige Flüge Marketing GmbH Emanuelstr. 3, 10317 Berlin Deutschland Telefon: +49 (33) 5310967 Email: utebachmeier at gmail.com Site: http://flug.airego.de - Billige Flüge vergleichen

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downloading pre-indexed genomes to our galaxy server
by Nikhil Joshi 06 Sep '11

06 Sep '11

Hi all, Is there a repository of pre-indexed genomes for base-space/color-space, bwa, bam, sam, etc...? It would be much easier than having to index them all ourselves.... :) - Nik.

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handling galaxy updates
by Shantanu Pavgi 06 Sep '11

06 Sep '11

Hi, I am curious to know which revision of galaxy code gets deployed in the main ( http://main.g2.bx.psu.edu/ ) and test ( http://test.g2.bx.psu.edu/ ) instances of galaxy. I was thinking active development repository galaxy-central code gets deployed in the test galaxy instance and stable galaxy-dist code gets deployed in the main galaxy instance. However, it seems like main galaxy instance is updated more frequently than galaxy-dist repository. Should local galaxy instances keep up with PSU's main galaxy instance revisions or wait for stable code to be released in galaxy-dist repository? We have been keeping up with galaxy-dist repository and not the galaxy-central repository updates. Are other sites following similar update model? -- Thanks, Shantanu.

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link file bug in the new version
by remy d1 06 Sep '11

06 Sep '11

Hi, We found a little problem in the new galaxy release. When we upload a dataset library from filesystem : Admin > Manage data libraries > create new data library > Add dataset > Upload files from filesystem path > Link to files without copying If galaxy user is the owner of this file or if he has write permission on it (on the filesystem), the file is deleted !! I do not think it is the normal behaviour... Regards.

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rpy - No module named rpy CentoOs install
by Joseph Hargitai 06 Sep '11

06 Sep '11

Hi, On our Ubuntu install stat packages and all that require rpy work fine. On our CentOs install seeing this stubborn error that I did see from previous post to be difficult to fix. At first suspected the SGE issue - environment not transferring to compute nodes. After changing the app to run local had the same issue. CentOs: 2.6.18-92.1.13.el5 rpy module is in: /apps1/python/2.6.6/intel/lib/python2.6/site-packages _rpy2122.so _rpy2131.so version: [galaxy@compute-0-65 galaxy-dist]$ python -c "import rpy; print rpy.__version__" 1.5.1 path: python -c 'import sys; print "\n".join( sys.path )' /apps1/python/2.6.6/intel/lib/python2.6/site-packages/simplejson-2.0.9-py2.6-linux-x86_64.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/Sphinx-1.0.7-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/docutils-0.7-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/Jinja2-2.5.5-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/Pygments-1.4-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/nose-1.0.0-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/Traits-3.5.0-py2.6-linux-x86_64.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/nibabel-1.0.0-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/nipype-0.0.0-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/setuptools-0.6c12dev_r88846-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/birdsuite-1.0-py2.5.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/mpgutils-0.7-py2.5.egg /apps1/python/2.6.6/intel/lib/python26.zip /apps1/python/2.6.6/intel/lib/python2.6 /apps1/python/2.6.6/intel/lib/python2.6/plat-linux2 /apps1/python/2.6.6/intel/lib/python2.6/lib-tk /apps1/python/2.6.6/intel/lib/python2.6/lib-old /apps1/python/2.6.6/intel/lib/python2.6/lib-dynload /apps1/python/2.6.6/intel/lib/python2.6/site-packages /apps1/python/2.6.6/intel/lib/python2.6/site-packages/PIL compiled against /R/2.13.1 env: export PATH=.:\ /apps1/R/2.13.1/intel/bin:\ /apps1/python/2.6.6/intel/bin:\ /apps1/pipe/bowtie/0.12.7/intel:\ /apps1/pipe/bwa/0.5.9/intel:\ /apps1/samtools/0.1.13/intel/bin:\ /apps1/fastx_toolkit/0.0.13/intel/bin:\ /apps1/maq/maq-0.7.1:\ /apps1/maq/maq-0.7.1/scripts:\ /apps1/bfast/bfast-0.6.5a/butil:\ /apps1/bfast/bfast-0.6.5a/scripts:\ /apps1/abyss/1.2.7/intel/bin:\ /apps1/velvet/velvet_1.0.12:\ /apps1/pipe/tophat/1.3.0/intel/bin:\ /apps1/pipe/cufflinks/1.0.3/intel/bin:\ /apps1/blast/2.2.25/gnu/bin:\ /apps1/blast+/2.2.5/gnu/bin:\ /apps1/sputnik/intel/bin:\ /apps1/taxonomy/intel/bin:\ /apps1/add_scores/add_scores:\ /apps1/emboss/6.4.0/intel/bin:\ /apps1/hyphy/hyphy/HYPHY:\ /apps1/lastz/1.02.00:\ /apps1/perm/0.3.6/intel/bin:\ /apps1/beam2/intel/bin:\ /apps1/pass2/intel/bin:\ /apps1/plink/1.07/intel/bin:\ /apps1/fbat/2.0.3/bin:\ /apps1/eigensoft/3.0/intel/bin:\ /apps1/mosaik/Mosaik-1.1.0021-Linux-x64/bin:\ /apps1/freebayes/freebayes.git/bin:\ $PATH export LD_LIBRARY_PATH=.:\ /apps1/python/2.6.6/intel/lib:\ /apps1/libgtextutils/0.6/intel/lib:\ /apps1/emboss/6.4.0/intel/lib:\ /apps1/intel/lib/intel64:\ /apps1/intel/mkl/lib/em64t:\ /apps1/tcltk/8.5.9/intel/lib:\ /apps1/zlib/1.2.5/intel/lib:\ /apps1/graphviz/2.26.3/intel/lib:\ /apps1/python/2.6.6/intel/lib/python2.6/site-packages/simtk/chem/openmm/OpenMM:\ /apps1/python/2.6.6/intel/lib/python2.6/site-packages:\ /apps1/libpng/1.5.0/intel/lib:\ /apps1/R/2.13.1/intel/lib64/R/lib:\ $LD_LIBRARY_PATH export PKG_CONFIG_PATH=.:\ /apps1/R/2.13.1/intel/lib64/pkgconfig:\ /apps1/libgtextutils/0.6/intel/lib/pkgconfig:\ /apps1/sparsehash/1.11/intel/lib/pkgconfig:\ $PKG_CONFIG_PATH export CLASSPATH=.:\ /apps1/gatk/gatk-git/dist:\ /apps1/gatk/gatk-git/lib:\ /apps1/srma/srma-0.1.13:\ /apps1/haploview/4.2:\ /apps1/picard/picard-tools-1.50:\ /apps1/fastqc/fastqc-0.9.5:\ $CLASSPATH best, joe

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