> On 5/8/13 20:08:08.000, Ira Cooke wrote:
>>
>> Hi All,
>>
>> I'm starting to add functional tests to my tools but I've found that I
>> can't get the test framework to work well with tool dependencies.
>>
>> The tool I'm considering is xtandem
>>
>> http://testtoolshed.g2.bx.psu.edu/view/iracooke/xtandem
>>
>> When I install this tool on my local galaxy instance (on a clean install)
>> the tool runs fine and if I look in the handler logs I see
>>
>> executing:
>> PACKAGE_BASE=/home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab;
>> export PACKAGE_BASE; .
>> /home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab/env.sh;
>> PACKAGE_BASE=/home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab;
>> export PACKAGE_BASE; .
>> /home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab/env.sh;
>> rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d
>> /home/iracooke/galaxy-central/database/files/000/dataset_1.dat
>> --var-mods='            57.021464__at__C                '       --fix-mods='
>> 15.994915__at__M                '
>> /home/iracooke/galaxy-central/database/files/000/dataset_2.dat -o
>> /home/iracooke/galaxy-central/database/files/000/dataset_4.dat -r
>> --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0
>> --strict-monoisotopic-mass --keep-params-files
>> galaxy.jobs DEBUG 2013-04-27 06:53:35,586 (4) Persisting job destination
>> (destination id: local:///)
>>
>>
>> Note that in this case the tool environments from my tool dependencies are
>> loaded ... and the tool runs fine.
>>
>> When running functional tests however the tests are executed without first
>> loading the environments from tool dependencies ... and naturally the tool
>> fails.  On my local machine I get the following when running the tests (Note
>> that no loading of dependency shel environments occurs).  (This seems to be
>> the same issue on the testtoolshed.g2.bx.psu.edu ).
>>
>> Job dispatched
>> galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,564 (3) executing: rvm
>> 1.9.3@protk-1.2.0 do tandem_search.rb -d
>> /tmp/tmp3I8GgN/database/files/000/dataset_1.dat             --var-mods='
>> 15.994915__at__M                ,               '               --fix-mods='
>> 57.021464__at__C                '
>> /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o
>> /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin
>> --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0
>> --strict-monoisotopic-mass --keep-params-files
>> galaxy.jobs DEBUG 2013-04-27 06:55:19,730 (3) Persisting job destination
>> (destination id: local:///)
>> galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,889 execution
>> finished: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d
>> /tmp/tmp3I8GgN/database/files/000/dataset_1.dat                --var-mods='
>> 15.994915__at__M                ,'              --fix-mods='
>> 57.021464__at__C                '
>> /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o
>> /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin
>> --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0
>> --strict-monoisotopic-mass --keep-params-files
>> ...
>> galaxy.jobs DEBUG 2013-04-27 06:55:24,277 setting dataset state to ERROR
>>
>>
>> Is there something wrong with the way I've defined my tool dependencies
>> for this tool?  Or perhaps it's a bug in the testing framework.
>>
>> Cheers
>> Ira

On Thu, May 9, 2013 at 3:10 PM, Dave Bouvier <d...@bx.psu.edu> wrote:
> Ira,
>
> There is a known issue with resolving tool dependencies when running
> functional tests. One workaround is to set the GALAXY_TOOL_DEPENDENCY_DIR
> environment variable to the path configured in your universe_wsgi.ini.
>
> This issue is documented in https://trello.com/c/eVT3QWJF
>
>    --Dave B.

Does this issue affect the Tool Shed tests as well, or just when run
via run_functional_test.sh? (I'm working though a couple of test
failures related to the dependency installation breaking somehow).

Thanks,

Peter
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