On Jan 19, 2012, at 12:57 AM, Fields, Christopher J wrote:
Just to add for the list, nate mentioned on IRC that running tests on an external server likely doesn't work at the moment but that ./scripts/functional_tests.py may have something to work with via environment variables.
The tool config can be specified in: $GALAXY_TEST_TOOL_CONF The config file is a bit trickier since many Galaxy config options can be overridden by environment variables or are set to something other than the normal default right in functional_tests.py. You could change this line (147): global_conf = { '__file__' : 'universe_wsgi.ini.sample' } To change the config default, however. --nate
chris
On Jan 18, 2012, at 8:03 PM, Fields, Christopher J wrote:
Greg,
That seems to work mainly for running tests from the sample universe/tool config files, so it uses the local job runner. What I would like to do is run tests using the actual Galaxy server configuration (which might use PBS/DRMAA and a cluster). The method I mention from that page seemed to be for that purpose, but again it seems possibly out-of-date...
chris
On Jan 18, 2012, at 4:20 PM, Greg Von Kuster wrote:
Hello Chris,
You should be able to run functional tests from the Galaxy install directory using the following from the command line.
%sh run_functional_tests.sh
There are several options you can use as well.
Greg
On Jan 18, 2012, at 4:38 PM, Fields, Christopher J wrote:
I have been following the basic protocol for running remote tests on a Galaxy server (in this case, our local one) using:
http://wiki.g2.bx.psu.edu/Admin/Running%20Tests
From reading this, I assume the tests are to be run from the galaxy root directory, like so:
GALAXY_TEST_EXTERNAL=1 GALAXY_TEST_HOST=my.local.galaxy.url GALAXY_TEST_PORT=8080 \ ./nosetests.sh
However, no 'nosetests.sh' script exists there. Should we be using ./scripts/nosetests.py? ./scripts/functional_tests.py?
Any clarification on this would be very helpful, we're just searching for a way to run tests in as automated a way as possible using the server configuration.
chris
Chris Fields Senior Research Scientist National Center for Supercomputing Applications Institute for Genomic Biology University of Illinois at Urbana-Champaign
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Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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