diff --git a/README.md b/README.md index 57ad76ed184b46b0cc29f6311b4e658c9842fdf3..6f4e1d1ff9467c7ccd0ac6e0537d998fa502a7f5 100644 --- a/README.md +++ b/README.md @@ -6,6 +6,14 @@ This a snakemake pipeline allowing to reconstruct the 6-chips data automatically ## 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 ``` @@ -13,5 +21,7 @@ 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``` +In another terminal you can see the status of the jobs using *sacct* +``` +watch sacct +```