singularity support #844
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singularity support #844
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Maarten-vd-Sande
changed the title
siebrenf
approved these changes
Apr 28, 2022
| @@ -1,6 +1,7 @@ | |||
| """ | |||
| all logic not related to any specific workflows should be here. | |||
| """ | |||
| container: "docker://quay.io/biocontainers/seq2science:0.7.2--pypyhdfd78af_0" | |||
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this won't break anything right?
| @@ -1,4 +1,4 @@ | |||
| #!/usr/bin/perl | |||
| #!/usr/bin/env perl | |||
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might need to add/change shebangs to other scripts too
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What problem is the PR solving / What's new?
Let's maybe merge this just so I can do more testing with singularity 馃槆 (after a new release we get an automatic singularity container made for us), we won't add any documentation abuot singularity (yet). A nice addition is that it improves some envs of which not all requirements were properly defined.
Support for singularity should be relatively easy with this:
https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#ad-hoc-combination-of-conda-package-management-with-containers
related: snakemake/snakemake#1588
Still needs plenty of streamlining, especially to be able to run seq2science itself from singularity, to test currently:
export SINGULARITY_BIND="/scratch/${USER},${CONDA_PREFIX},${TMPDIR},${XDG_CACHE_HOME}"seq2science run rna-seq --cores 20 --snakemakeOptions use_singularity=True conda_prefix=/scratch/sande/singularity_test/envsChecklist