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Docker cheatsheet

Build.

docker build -t plancha-workflow:latest . docker tag plancha-workflow:latest seatizendoi/plancha-workflow:latest docker push seatizendoi/plancha-workflow:latest

docker build -t plancha-workflow:latest . && \
docker tag plancha-workflow:latest seatizendoi/plancha-workflow:latest && \
docker push seatizendoi/plancha-workflow:latest

Run.

Command to just open container : docker run --rm plancha-workflow:latest bash

Command to link volume with container : docker run --rm -v /home/bioeos/Documents/Bioeos/plancha-session:/home/seatizen/plancha plancha-workflow:latest bash docker run -v /home/bioeos/Documents/Ifremer/plancha:/home/seatizen/plancha plancha-workflow:latest

If entrypoint is set, launch command without bash.

Command with session_name docker run --rm -v /home/bioeos/Documents/Bioeos/plancha-session:/home/seatizen/plancha plancha-workflow:latest [OPTIONS WORKFLOW.PY]

Singularity cheatsheet

Datarmor, the ifremer supercomputer, doesn't handle custom docker image easily. You need to convert your docker image to a singularity container.

Build container.

singularity build -f workflow.sif docker://seatizendoi/plancha-workflow:latest singularity build -f --sandbox workflow.sif docker://seatizendoi/plancha-workflow:latest

Launch container.

singularity run --bind /home1/datawork/villien/plancha-session:/home/seatizen/plancha workflow.sif