Oops ... I should have thought of that Thanks .. it works now.
Ira On 04/06/2013, at 11:20 PM, Dave Bouvier <d...@bx.psu.edu> wrote: > 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 >>>> >>>> >>>> >>>> >>>> >>>> >>>> ___________________________________________________________ >>>> Please keep all replies on the list by using "reply all" >>>> in your mail client. To manage your subscriptions to this >>>> and other Galaxy lists, please use the interface at: >>>> http://lists.bx.psu.edu/ >>>> >>>> To search Galaxy mailing lists use the unified search at: >>>> http://galaxyproject.org/search/mailinglists/ >>>> >> >> ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
