Hi all, I’m making baby steps towards having a repeatable installation for my tools. But I’m now stuck, so help would be appreciated.
I have a tool that works and is in the test toolshed (alveoimport in Data Sources).
It depends on my python package which is now part of bioconda (pyalveo, version 0.6).
I can run my tool via planemo, which works I think because I have pyalveo installed in a local venv.
If I try to run the docker image (derived from bgruening/galaxy-stable but with the testtoolshed added) I am able to install my tool, but it doesn’t pick up the dependency, so it doesn’t work.
I tried running with planemo turning on conda dependency resolution (following https://pypi.python.org/pypi/planemo/):
planemo serve --galaxy_branch release_16.01 --conda_dependency_resolution .
It seems to have a go, but fails:
galaxy.tools.deps DEBUG 2016-08-25 17:32:22,449 Building dependency shell command for dependency 'pyalveo' galaxy.tools.deps DEBUG 2016-08-25 17:32:22,449 Find dependency pyalveo version 0.6 galaxy.tools.deps DEBUG 2016-08-25 17:32:22,450 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x105bef5d0> (isnull? True) galaxy.tools.deps DEBUG 2016-08-25 17:32:22,450 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x105bef5d0> (isnull? True) galaxy.tools.deps WARNING 2016-08-25 17:32:22,451 Failed to resolve dependency on 'pyalveo', ignoring
So, what’s the easiest route to a Galaxy deployment with my tool installed. The Docker route would be best I think, but what do I have to add to bgruening/galaxy-stable to have conda find my dependencies.
Thanks in advance,
Steve
— Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy