Containerize using snakemake i.e., add a Dockerfile?
does not cost anything, can be automatically created (every time something changes in the software)
[ ] automatize this step using GitHub actions?
[ ] Singularity ****support: use singularity functionality to automatically create a container and set it up on DockerHub to trigger image build
[x] issue in rule_all: /usr/bin/bash: line 1: snakemake: command not found
two solutions: install snakemake additionally (snakemake inception?!) or manual report generation (if this, what signals the successful completion to the user?) → solved
[ ] issue: errors occur immediately when submitting jobs with singularity: try it with local execution only → works (suspicion: module singularity is not loaded in the jobs → it is...)
[ ] idea from PC
you could always try the exact opposite:
put export SBATCH_EXPORT=ALL
in your .bashrc, open a new terminal, activate a new conda env, start a new jupyterhub interactive job, and then launch snakemake
modules