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/

Reply via email to