diff --git a/.gitignore b/.gitignore index 391eea7c53ef674b8200f4ac68c098989273b843..939b39609b64370dd3a8ef7a8ad78cd5b7007483 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,4 @@ +.RData +.Rhistory *~ *\.wrapper\.py diff --git a/run_pipeline.sh b/run_pipeline.sh index ff7681f308c71c1db3eb4d7f67fd65f5136d1a5d..38637d4768d05be93dba07f0f2b009c864841c55 100755 --- a/run_pipeline.sh +++ b/run_pipeline.sh @@ -82,6 +82,10 @@ config_base=$(basename ${configfile}) config_snapshot="${output_dir}/${config_base}" echo "Saving a local copy of the configuration in ${config_snapshot}" cp -f ${configfile} ${config_snapshot} +snakefile_base=$(basename ${snakefile}) +snakefile_snapshot="${output_dir}/${snakefile_base}" +echo "Saving a local copy of the snakefile in ${snakefile_snapshot}" +cp -f ${snakefile} ${snakefile_snapshot} kilobytes_tot=$(mawk '$1 == "MemTotal:" {print $2}' /proc/meminfo) # Some rules were given a "mem_mb" resource section based on the "max_vms" benchmarking result. @@ -91,7 +95,9 @@ kilobytes_tot=$(mawk '$1 == "MemTotal:" {print $2}' /proc/meminfo) # to avoid pretending that we have all this memory available for snakemake rules. megabytes_resource=$(echo "${kilobytes_tot} / 1100" | bc) -cmd="(cd ${output_dir}; snakemake -s ${snakefile} --configfile ${config_base} --resources mem_mb=${megabytes_resource} $@)" +#cmd="(cd ${output_dir}; snakemake -s ${snakefile} --configfile ${config_base} --resources mem_mb=${megabytes_resource} $@)" +# TODO: check that this works +cmd="(cd ${output_dir}; snakemake -s ${snakefile_base} --configfile ${config_base} --resources mem_mb=${megabytes_resource} $@)" echo ${cmd} > ${log_base}.log # https://unix.stackexchange.com/a/245610/55127