And remap the $tool_directory into a fixed internal path?
$__tool_directory__ is the path to the directory where the wrapper lives. I don’t know what remapping to a fixed interal path means
~/src/galaxy/tools shed_indexing_fix_for_python2 ? find . -name \*.py|wc -l 84 ~/src/galaxy/tools shed_indexing_fix_for_python2 ? find . -name \*.sh|wc -l 7 ~/src/galaxy/tools shed_indexing_fix_for_python2 ? find . -name \*.pl|wc -l 19 ~/src/galaxy/tools shed_indexing_fix_for_python2 ? find . -name \*.R|wc -l
$__tool_directory__on the jobs’ PATH, collect all wrapper scripts with symlinks in in a package and then change
$__tool_directory__/wrapper.pyto just say
wrapper.pyand annotate the tools with a requirement on this new package
tools/folder in your deployments ?
So wrt to the concern you raised about implicit dependencies, what if there was a variant on dependencies like this:
Sort of like the old code tag. I always thought it would be nice to capture the fact that the wrapper relies on an external file like this somewhat more explicitly. The conda package for them could be implicit and synced to the tool wrapper’s version.
/cvmfs/main.galaxyproject.org/galaxy/tools/filters/join.py, which is already mounted into the job containers. Assuming the code there is kept up to date, can't we universally point to the galaxy code on the CVMFS for any wrapper portion requiring gxy code? Unless i'm misunderstanding the problem