Ira,
Yes, I should have mentioned that due to the way functional tests are
executed, an environment variable needs to be explicitly exported before
the functional test framework will recognize it. The syntax is very
nearly the same:
export GALAXY_TOOL_DEPENDENCY_DIR=/home/iracooke/tool_dependencies ; sh
run_functional_tests.sh -installed
--Dave B.
On 6/3/13 00:25:53.000, Ira Cooke wrote:
Hi Dave,
Just following up on this (now quite a bit later sorry).
I can't seem to get things to work using your suggested workaround.
Using a fresh checkout of galaxy-central 9931:716f29e4c77d
I run
GALAXY_TOOL_DEPENDENCY_DIR=/home/iracooke/tool_dependencies sh
run_functional_tests.sh -installed
In my universe_wsgi.ini I have
tool_dependency_dir = /home/iracooke/tool_dependencies
When running tests I find that the dependencies fail to be resolved (ie ... I
get errors like the following).
galaxy.jobs.handler INFO 2013-04-28 11:01:17,955 (3) Job dispatched
galaxy.tools DEBUG 2013-04-28 11:01:18,594 Building dependency shell command
for dependency 'galaxy_protk'
galaxy.tools WARNING 2013-04-28 11:01:18,595 Failed to resolve dependency on
'galaxy_protk', ignoring
galaxy.tools DEBUG 2013-04-28 11:01:18,596 Building dependency shell command
for dependency 'trans_proteomic_pipeline'
galaxy.tools WARNING 2013-04-28 11:01:18,596 Failed to resolve dependency on
'trans_proteomic_pipeline', ignoring
When I run the tool myself (ie from galaxy ui not from the test script) it
resolves the dependencies just fine.
Any idea what am I doing wrong?
Thanks
Ira
On 10/05/2013, at 12:10 AM, 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.
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
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