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iqbal-lab-org / make_prg

Code to create a PRG from a Multiple Sequence Alignment file
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Singularity container can't be run in snakemake pipelines #20

Closed leoisl closed 1 year ago

leoisl commented 3 years ago

I tried to run the make_prg singularity container (latest) in a snakemake pipeline, but got an issue. snakemake run the container as (we necessarily need bash):

Command ' singularity exec --home <suppressed> bash -c 'set -euo pipefail;  python /home/leandro/git/myforks/pandora_analysis_pipeline/.snakemake/scripts/tmp_b7uof0h.run_make_prg.py'' returned non-zero exit status 255.

Error is:

FATAL:   "bash": executable file not found in $PATH

Upon further inspection of the container, indeed bash not only cannot be found in $PATH, but it is not installed at all, which seems weird to me, as this line: https://github.com/rmcolq/make_prg/blob/c00fc137456aa474f2f75dd23e1f10c08876dfe9/Singularity#L12 seems to install it

mbhall88 commented 3 years ago

Oh, I don't think I had updated the latest tag to the actual latest container.

"library://mbhall88/default/make_prg:0bb4a27" is actually the latest and has bash installed. Although this is not the tip of master. I have not been updating the container inline with the github repo as I am using a fixed commit.

Ultimately, we should have this set to build a docker container and push to quay.io on pushing a tag to github.

leoisl commented 1 year ago

Closing, outdated