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Peregrine: Fast Genome Assembler Using SHIMMER Index
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Run peregrine with singularity #37

Open RenzoTale88 opened 3 years ago

RenzoTale88 commented 3 years ago

Good evening, I need to run singularity, and I'd like to use the containerised version since easier to implement. I can successfully pull the image with 

singularity pull peregrine.sif docker://cschin/peregrine:latest

But when I try to run it with exec:

singularity exec peregrine.sif pg_run.py

I get the following error:

INFO:    Convert SIF file to sandbox...
/.singularity.d/actions/exec: 21: exec: pg_run.py: not found
INFO:    Cleaning up image...

Is there a way to implement the software using singularity instead of docker?

Thank you in advance Andrea

ASLeonard commented 3 years ago

It appears pg_run.py is only visible after the conda env is activated in the entry script (see /opt/entry.sh in the container). It works fine if you do 

singularity run [singularity options] peregrine_latest.sif asm [peregrine options]

Otherwise you could include the activation steps in the exec command.