Trying to solve memory issues.

This is actually related to 16b41b3f.

run_pipeline.sh

@@ -67,7 +67,14 @@ shift
 
 if [ -e ${configfile} ]
 then
-    cmd="snakemake -s ${snakefile} --configfile ${configfile} $@"
+    kilobytes_tot=$(mawk '$1 == "MemTotal:" {print $2}' /proc/meminfo)
+    # Some rules were given a "mem_mb" resource section based on the "max_vms" benchmarking result.
+    # See the /pasteur/homes/bli/Documents/Informatique/benchmarks/Pipeline_benchmarking/Pipeline_benchmarking.ipynb jupyter notebook.
+    # These values are in megabytes (https://stackoverflow.com/a/47201241/1878788)
+    # We divide the total memory (in kB) by 1100 instead of 1000
+    # to avoid pretending that we have all this memory available for snakemake rules.
+    megabytes_resource=$(echo "${kilobytes_tot} / 1100" | bc)
+    cmd="snakemake -s ${snakefile} --configfile ${configfile} --resources mem_mb=${megabytes_resource} $@"
 else
     error_exit "Pipeline configuration file ${configfile} not found."
 fi