Hi Steve, you call this baby-steps? I think this is huge! :)
All what you are missing is to enable conda in Galaxy. Look at Gregs new flavour which is entirely Conda/Galaxy based. You need to enable these env vars to make Galaxy conda enabled: https://github.com/gregvonkuster/docker-galaxy-csg/blob/master/Dockerfile#L9 Hope this helps, Bjoern Am 25.08.2016 um 12:32 schrieb Steve Cassidy: > 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 > <http://web.science.mq.edu.au/%7Ecassidy> > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
