I was able to partially solve this by running a small command to source all my "env.sh" files before I run all the tests. For example:
export GALAXY_TOOL_DEPENDENCY_DIR=/path/to/tool-dependencies for i in `find $GALAXY_TOOL_DEPENDENCY_DIR -iname 'env.sh'`; do source $i; done sh run_functional_tests.sh -installed Not sure if it's the best way to handle things, but it works for now. Aaron On Fri, Jul 11, 2014 at 2:54 PM, Aaron Petkau <aaron.pet...@gmail.com> wrote: > 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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