Problem with tool dependencies when running functional tool tests

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Problem with tool dependencies when running functional tool tests

Peter Briggs
Hello again

As an addendum to my previous message, I'm also having general problems
running the functional tests for any tool, due to unresolved tool
dependencies.

For example if I clone and configure a fresh galaxy-dist instance and
install the FastQC tool from the main toolshed, and then run e.g.:

$ export
GALAXY_TOOL_DEPENDENCY_DIR=/home/pjb/galaxies/kellerman/tool_dependencies ;
sh run_functional_tests.sh -installed

In the stdout I see output like:

...
galaxy.tools.deps: DEBUG: Building dependency shell command for
dependency 'FastQC'
galaxy.tools.deps: WARNING: Failed to resolve dependency on 'FastQC',
ignoring
...

and in the run_functional_tests.html report I see:

Traceback (most recent call last):
   File
"/home/pjb/galaxies/kellerman/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/e28c965eeed4/fastqc/rgFastQC.py",
line 204, in <module>
     assert os.path.isfile(opts.executable),'##rgFastQC.py error -
cannot find executable %s' % opts.executable
AssertionError: ##rgFastQC.py error - cannot find executable /fastqc

As far as I can make out I'm correctly following the instructions at

        https://wiki.galaxyproject.org/TestingInstalledTools

so I'm wondering if anyone can point out what it is that I'm missing. No
doubt it's blindingly obvious, but I just can't see it.

Thanks again for any help

Peter

--
Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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