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