Add SBATCH env variable.

This is an attempt to make it possible to run the main snakemake command
using sbatch. When calling the script, the content of the SBATCH
variable will be pre-pended to the main snakemake call (not the one used
to generate the rulegraph).

run_pipeline.sh

@@ -114,7 +114,7 @@ megabytes_resource=$(echo "${kilobytes_tot} / 1100" | bc)
 from_dir=$(pwd)
 #cmd="(cd ${output_dir}; snakemake -s ${snakefile} --configfile ${config_base} --resources mem_mb=${megabytes_resource} $@)"
 # TODO: check that this works
-cmd="(cd ${output_dir}; echo ${USER}@${HOSTNAME}:${from_dir}/${output_dir} > pwd.txt; snakemake -s ${snakefile_base} --configfile ${config_base} --rulegraph | dot -Tpdf > rulegraph.pdf; snakemake -s ${snakefile_base} --configfile ${config_base} --resources mem_mb=${megabytes_resource} $@)"
+cmd="(cd ${output_dir}; echo ${USER}@${HOSTNAME}:${from_dir}/${output_dir} > pwd.txt; snakemake -s ${snakefile_base} --configfile ${config_base} --rulegraph | dot -Tpdf > rulegraph.pdf; ${SBATCH} snakemake -s ${snakefile_base} --configfile ${config_base} --resources mem_mb=${megabytes_resource} $@)"
 
 echo ${cmd} | tee -a ${log_base}.log
 # https://unix.stackexchange.com/a/245610/55127