- Load slurm and miniconda
ml slurm
ml miniconda
2A) FIRST TIME ONLY: Setup environment
conda env create -f workflow/envs/qc_trim_align.yml
2B) Start environment:
conda activate qc_trim_align
-
Modify the config/config.yml
-
Modify the samples.csv
-
Test with dry run
snakemake -npr
- Run with slurm
sbatch --wrap="\
snakemake \
-R \
-j 999 \
--cluster-config config/cluster_config.yml \
--cluster '\
sbatch \
-A {cluster.account} \
-p {cluster.partition} \
--cpus-per-task {cluster.cpus-per-task} \
-t {cluster.time} \
--mem {cluster.mem} \
--output {cluster.output}'"
- When finished, exit environment.
conda deactivate