Commit cd18464c authored by Christian Meesters's avatar Christian Meesters

LA_Wrapper: updated version and history info

parent 40cbb30b
......@@ -52,7 +52,7 @@ module load bio/BLAST+/2.9.0-gompi-2019a
### setup variable for THIS script; giving absolute path if necessary
SCRIPT="$0"
SCRIPT_VERSION="0.5.1"
SCRIPT_VERSION="0.5.3"
# TODO: delete the following 3 functions, once sbcast is working
function queue {
......@@ -135,6 +135,7 @@ _arg_blastdir='.'
_arg_executable='blastx'
_arg_test=off
_arg_compress=on
_arg_debug=off
print_help ()
{
......@@ -225,6 +226,7 @@ credits()
echo "- v0.5.2 -- 02. Sep. 2019 -- fix:"
echo " - consistent biopython inclusion"
echo " - auto-detection of database size and memory selection"
echo "- v0.5.3 -- 24. Sep. 2019 -- fix: dereferencing of reference / database files re-enabled"
echo
echo "Current version is: $SCRIPT_VERSION"
echo
......@@ -414,6 +416,10 @@ do
_arg_test="on"
test "${1:0:5}" = "--no-" && _arg_test="off"
;;
--debug)
_arg_debug="on"
set -x
;;
--credits|--version)
credits
exit 0
......@@ -661,7 +667,13 @@ if [ -z "$SLURM_JOB_ID" ]; then
export SCRIPT_PATH=$(dirname $0)
submit_statement="sbatch -o ${JOBTAG}_%j.out -J $JOBTAG -p $_arg_queue -A $_arg_assoc -t $_arg_runlimit -N $_arg_nodes -n $((64 * $_arg_nodes / $threads)) --mem=$_memory_request --ramdisk=${_arg_ramdisk} -c $threads"
script_statement="$SCRIPT --partition $_arg_queue --account $_arg_assoc --nodes $_arg_nodes --time $_arg_runlimit --reservation=$_arg_reservation --threads $_arg_blast_threads --splitup $_arg_splitup_per_queryfile --blastparams=\"$BLASTPARAMS\" --executable=$_arg_executable $FASTA $DATABASE"
script_statement="$SCRIPT --partition $_arg_queue --account $_arg_assoc --nodes $_arg_nodes --time $_arg_runlimit --reservation=$_arg_reservation --threads $_arg_blast_threads --splitup $_arg_splitup_per_queryfile --blastparams=\"$BLASTPARAMS\" --executable=$_arg_executable "
if [[ $_arg_debug == "on" ]]; then
script_statement="${script_statement} --debug"
fi
# supply the input files regarless of any user request:
script_statement="${script_statement} $FASTA $DATABASE"
if [ -n "$_arg_reservation" ]; then
submit_statement="${submit_statement} --reservation=${_arg_reservation}"
fi
......@@ -783,15 +795,7 @@ parallel="parallel --no-notice -j $SLURM_NTASKS -P $SLURM_NTASKS "
srun="srun --cpu-bind=q --mem-bind=q -n 1 -N1 --exclusive -c $SLURM_CPUS_PER_TASK --jobid $SLURM_JOBID --mem-per-cpu=$((SLURM_MEM_PER_NODE / SLURM_CPUS_ON_NODE))"
$parallel "$srun" "$cmdfile" ::: $samples
echo before wait
echo $n_unfinished_files $_arg_compress $OUTOUT
wait
echo after wait
echo $n_unfinished_files $_arg_compress $OUTOUT
n_unfinished_files=$(comm -3 <(cd output && find .| grep -o '[0-9]*' |sort ) <(cd scratch && find . | grep -o '[0-9]*' |sort )|wc -l)
echo after setting
echo $n_unfinished_files $_arg_compress $OUTOUT
if [ $n_unfinished_files -eq 0 ] && [[ $_arg_compress == "on" ]] && [ $XMLOUT -eq 1 ]; then
# shrink the alloction, such that only the minimum necessary is accounted for
#scontrol update job=$SLURM_JOB_ID NumNodes=1
......
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