slurm

Author: metavannier

README.md

@@ -58,11 +58,11 @@ Configure the workflow according to your needs via editing the files and reposit
 
 #### On a cluster
 
-- Write the batch script to run your snakemake from the working directory
+- Adapt the batch scripts run_slurm.sh and cluster_config.json file to run your snakemake from the working directory
 
-It will create a snakemake virtual environment and install the packages needed with pip.
+It will install snakemake with pip and run the workflow in the HPC:
 
-`sbatch sc_rnaseq_slurm_skylake.sh`
+`sbatch run_slurm.sh`
 
 ### Step 4: Investigate results
 

Snakefile

@@ -1,3 +1,6 @@
+# Docker container based on a minimal Ubuntu installation that includes conda-forge's mambaforge installer.
+container: "docker://condaforge/mambaforge"
+
 import pandas as pd
 import numpy as np
 from snakemake.utils import validate, min_version

sc_rnaseq_slurm_skylake.sh renamed to run_slurm.sh

@@ -1,40 +1,22 @@
 #!/bin/sh
-#SBATCH -J Job_scrna
+#SBATCH -J Microbeannotator
 #SBATCH -p skylake
 #SBATCH -N 1
-#SBATCH -n 1
+#SBATCH -n 12
 #SBATCH -A a272
-#SBATCH -t 00:30:00
+#SBATCH -t 11:00:00
 #SBATCH -o ./%N.%x.out
 #SBATCH -e ./%N.%x.err
 
-# This script needs to be started from
-# the run directory
+# This script needs to be started from the run directory
 
 # Load the modules and start the virtual environment
 module load userspace/all
 module load python3/3.6.3
 module load singularity/3.5.1
 
-# Create a snakemake virtual environment if necessary
-if [ ! -d snakemake_virtenv/ ]
-then
-  bash 04_Workflow/create_snakemake_virtualenv.sh
-fi
-
-source /scratch/tvannier/sc-rnaseq/snakemake_virtenv/bin/activate
-
-#export PATH=/scratch/tvannier/sc-rnaseq/snakemake_virtenv/condabin:$PATH
-#export LD_LIBRARY_PATH=/scratch/tvannier/sc-rnaseq/snakemake_virtenv/condabin:$LD_LIBRARY_PATH
-
 pip install snakemake==6.3.0
-#pip install manager
 pip install pandas
-#pip install mamba
-
-# move to the working directory
-#cd /scratch/$SLURM_JOB_USER/sc-rnaseq/
-
 
 # ================================================
 # Run the workflow
@@ -46,7 +28,7 @@ snakemake --snakefile Snakefile \
 	--use-singularity \
 	--use-conda \
 	--conda-frontend conda \
-	--singularity-args="-B /scratch/$SLURM_JOB_USER/sc-rnaseq/" \
+	--singularity-args="-B /scratch/$SLURM_JOB_USER/inmed_dechevigny_scrnaseq/" \
 	--jobs 1 \
 	--latency-wait 20 \
 	--max-jobs-per-second 5 \
@@ -61,7 +43,3 @@ snakemake --snakefile Snakefile \
 		--mem-per-cpu {cluster.mem-per-cpu} \
 		--output {cluster.output} \
 		--error {cluster.error}' \
-
-deactivate
-
-