THIS WIKI IS FOR DEVELOPERS to take temporary notes.

For up-to-date information, please visit http://sequana.readthedocs.io

How to run sequana pipeline on IP cluster.

module use /pasteur/zeus/projets/p02/Sequana/modules
module load sequana

There is a git repository used behind the scene. You may need to type this command (once for all)

git config --global --add safe.directory /pasteur/zeus/projets/p02/Sequana/.condas/sequana_0.18/github/sequana-wrappers

You also need to tell apptainer/singularity the special directory /pasteur using binding. Type this command

export APPTAINER_BINDPATH="/pasteur"

add it to your .bash_profile for next time.

That's it. Time to try:

sequana_mapper --reference-file ref.fasta --aligner-choice bwa --input-directory data

wait and see. If everything was good:

cd mapper
sbatch mapper.sh

check that the run is on-going using e.g.

squeue -u YOURLOGIN

and the slurm* files . In case of errors; check the logs//slurm files.