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Commit 6a48dd58 authored by Rachel LEGENDRE's avatar Rachel LEGENDRE
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Update runme.sh

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...@@ -15,6 +15,7 @@ conda install -c anaconda pandas ...@@ -15,6 +15,7 @@ conda install -c anaconda pandas
conda install -c bioconda pysam conda install -c bioconda pysam
#run the workflow: #run the workflow:
## DEPRECATED, follow the readme.md
conda activate snakemake conda activate snakemake
module load graalvm/ce-java8-20.0.0 fastqc module load graalvm/ce-java8-20.0.0 fastqc
module load samtools/1.10 module load samtools/1.10
...@@ -28,8 +29,7 @@ module load MultiQC/1.9 ...@@ -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 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
#run the workflow without loading modules before (with --use-envmodules):
# or without module:
conda activate snakemake conda activate snakemake
#check the pipeline: #check the pipeline:
snakemake --use-envmodules -n snakemake --use-envmodules -n
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