Multichip-snakemake

This a snakemake pipeline allowing to reconstruct the 6-chips data automatically

Installation

Running locally

On Elissa computer find and launch the icon on the desktop "Snakemake". The terminal will open. The command to launch reconstruction:

snakemake -c12 D:\Andrey\Data\path_to_final_table.csv

For conveniense it is possible to drag and drop the folder into the terminal to get a valid path, then simply add the missing filename at the end.

Running on the cluster

ssh USERNAME@maestro.pasteur.fr
snk
snakemake --cluster "srun -c12" -j32 ~/Anchor/Lena/Data/20220531-MIC-e.coli-cipro/{1st,2nd}exp/final_table.csv --cores 12

In another terminal you can see the status of the jobs using sacct

watch sacct