From 6a48dd58cf27325e560cef3d68ac2bc0431da83a Mon Sep 17 00:00:00 2001 From: Rachel LEGENDRE <rachel.legendre@pasteur.fr> Date: Thu, 3 Feb 2022 13:44:56 +0100 Subject: [PATCH] Update runme.sh --- runme.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/runme.sh b/runme.sh index 099b641..9344d47 100644 --- a/runme.sh +++ b/runme.sh @@ -15,6 +15,7 @@ conda install -c anaconda pandas conda install -c bioconda pysam #run the workflow: +## DEPRECATED, follow the readme.md conda activate snakemake module load graalvm/ce-java8-20.0.0 fastqc module load samtools/1.10 @@ -28,8 +29,7 @@ module load MultiQC/1.9 sbatch -q hubbioit -p hubbioit snakemake --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} -q hubbioit -p hubbioit" -j 300 --nolock - -# or without module: +#run the workflow without loading modules before (with --use-envmodules): conda activate snakemake #check the pipeline: snakemake --use-envmodules -n -- GitLab