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Combination for update to scanpy tools IUC galaxy wrappers

Open pcm32 opened this issue 1 year ago • 2 comments

This aims to add a new container for these minor set of changes in tools-iuc/scanpy.

It should specifically match these new deps versions, which aim to mimic as much as possible the ones in the current mulled container used by the tool, but overcoming an issue with a matplotlib 3.7.

pcm32 avatar Apr 19 '23 09:04 pcm32

The tool with the changes will work in the older container, which has correct versions of everything, but the conda pinnings were necessary for galaxy installations that use conda (there a new install of the tool from zero would fail - and tests fail with the original tool and not using --biocontainers).

pcm32 avatar Apr 19 '23 09:04 pcm32

This setup fails running the following conda incantation:

conda install  -c 'conda-forge' -c 'bioconda'  'scanpy=1.7.1' 'matplotlib=3.6.3' 'anndata=0.7.5' 'loompy=2.0.17' 'leidenalg=0.8.3' 'pandas=1.5.3' --strict-channel-priority -p /usr/local --copy --yes --quiet

locally however (this is written by Galaxy itself), this works:

conda create -y --quiet --override-channels --channel conda-forge --channel bioconda --channel defaults --name mulled-v1-4917acbefebd6e54bdf84ac0c0b8b42aa54a7d2f008df0dd6a9eccf29d568f5c scanpy=1.7.1 matplotlib=3.6.3 anndata=0.7.5 loompy=2.0.17 leidenalg=0.8.3 pandas=1.5.3

(and so does mamba). So I wonder why this setup doesn't use defaults and why it enforces the strict channel priority.

@bgruening would you be able to use your super powers and push a container with the above packages please? Or is there away that I can indicate here to avoid the strict channel priority and include defaults as well? Thanks!

pcm32 avatar Apr 21 '23 15:04 pcm32