Hello everyone,

I've been trying to get some functional tests developed for my tools and
I'm trying to figure out how to properly run them.  I'm following the guide
at https://wiki.galaxyproject.org/TestingInstalledTools  but when I run the
functional tests against tools installed from my tool shed I get some
strange error messages like:

Can't open perl script "//find-repeats.pl": No such file or directory

It can't find the script because in the tool XML file it is being run using
an environment variable like

<command interpreter="perl">
  /\$VCF2PSEUDO/find-repeats.pl -l $length -p $pid $fasta > $out

The environment variable is set up in one of the dependency packages for
this tool.

If I set this environment variable manually "export VCF2PSEUDO=/path/to/dir"
and then run the tests with:

export GALAXY_TOOL_DEPENDENCY_DIR=tool_dependencies
sh run_functional_tests.sh -installed

Then all my tests properly work.

So, I'm wondering does the run_functional_tests.sh script setup the
environment for dependency packages for each tool?  Or is there something
I'm missing?

Thanks and sorry for the longing email.  I'm still new to setting up and
using functional tests in Galaxy,

Aaron
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