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.
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.
Is it possible (and how) for Galaxy to work with Arabidopsis genome?
Dr. Vesselin Baev
Research Assistant Professor
University of Plovdiv
Dept. Molecular Biology
Tzar Assen 24
Plovdiv 4000, BULGARIA
+359 32 261 (560)
+359 89 43 80 945
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?
Hi all, how can I set a size limit for data to be uploaded in galaxy?
Cogentech - Consortium for Genomic Technologies
via adamello, 16
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).
/home/www/galaxy/lib/galaxy/eggs/__init__.py:529: UserWarning: Module
simplejson was already imported from
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.
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?