Thanks Nate.
I have tried that but it seems to run into problems with the expected output. This may be
simply the aforementioned python dependency issues, but I'll have to investigate more
in the coming week when I have time.
Just to get an idea of what I would like, I mainly want the capability to run tests on
(for instance) a new Galaxy deployment on an already-established cluster or other similar
conditions where tools may not be configured correctly (e.g. missing secondary
dependencies) or subtle versioning issues exist (e.g. wrong version of cufflinks).
I'm thinking this could eventually lead to a mechanism where one optionally generates
a tools_conf file that comments out or removes tool configurations not working properly,
as well as generates a report of the issues found (as run_functional_tests already does).
chris
On Jan 20, 2012, at 8:54 AM, Nate Coraor wrote:
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out-of-date...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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>>>>
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>>>
>>> Greg Von Kuster
>>> Galaxy Development Team
>>> greg(a)bx.psu.edu
>>>
>>>
>>>
>>
>>
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>
>
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