fix UCSC table browser on usegalaxy.cz

[martenson]

it likely needs conda environment destination?

usegalaxy.org:
https://github.com/galaxyproject/usegalaxy-playbook/blob/9a55e60f9f602ce4e5a1acd825903ce3416593d7/env/common/templates/galaxy/config/tpv/defaults.yaml.j2#L59-L66

example fail: https://usegalaxy.cz/datasets/d53c4865a0fbc49e/details

[martindemko]

Or we could define own container for this and have it on CVMFS singularity.metacentrum.cz and use the params: container_override as in https://github.com/galaxyproject/usegalaxy-playbook/blob/9a55e60f9f602ce4e5a1acd825903ce3416593d7/env/common/templates/galaxy/config/tpv/defaults.yaml.j2#L73-L76

[martenson]

this is a data source tool, I suspect it will require local running

[martindemko]

Probably, but I wasn't addressing this. Only the fact that installing and maintaining conda would be more complex than maintaining one container and running it in Singularity, both locally. We already run a few tools locally using Singularity.

[martenson]

What I meant is that data_source tools are special, afaik they need some of Galaxy's code on path (https://github.com/galaxyproject/galaxy/blob/dev/tools/data_source/data_source.py)

I think Nate might have a container for it somewhere

[martindemko]

I just tried to move it to a local destination in TPV and it works, apparently no container needed: https://usegalaxy.cz/datasets/28ba4c378a32abdd/details
But I did only one test.