Open rhpvorderman opened 3 years ago
@rhpvorderman It should be possible to do that by updating lib/galaxy/tool_util/deps/conda_util.py
, let us know if you would like to take a stab at it.
Sure. No problem! I will put my container plans on hold until I fix this.
@nsoranzo I suppose there are no objections to backporting this back to the 21.01 branch?
Sure. No problem! I will put my container plans on hold until I fix this.
Thanks!
I suppose there are no objections to backporting this back to the 21.01 branch?
Fine by me!
I did some work here: https://github.com/galaxyproject/galaxy/compare/dev...rhpvorderman:bug11817
But it turns out this does not install 'activate' and therefore the environments can not be activated the usual way. The environments are functional and the stuff in the bin folder works, but changing this also means changing the way galaxy commands are run (no activating, but simple path prepending should be done). So this is a less trivial issue than expected.
The debug output shows that conda uses the
-n
flag instead of the-p
flag to create the environments. This will always create the environment at the location whereconda
is installed. It is not possible to haveconda_prefix
andconda_exec
in a different prefix.In theory it should be possible to do the following:
This allows having the galaxy conda prefixes independent and separate of the root conda prefix. This is advantageous in containers.
I tried to do this, but it is not possible unfortunately.