Running development and live servers side-by-side
by Chris Cole
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
12 years, 2 months
Galaxy and Arabidopsis
by Vesselin Baev
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/
12 years, 2 months
SecurityFeatures - admin_users
by Andrew Olson
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
12 years, 2 months
Using SGE cluster
by Henrikki Almusa
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
12 years, 2 months
set an upload size limit
by Davide Cittaro
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
*/
12 years, 2 months
About adding tools
by Henrikki Almusa
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
12 years, 2 months
passing SGE parameters
by Chris Cole
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
12 years, 2 months
Tabular output column headings
by Andrew Olson
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
12 years, 2 months
Simplejson reimport error
by Sean Davis
/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
12 years, 2 months
Multiple outputs
by Andrew Olson
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
12 years, 2 months
