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Commits (3)
......@@ -43,8 +43,7 @@ module purge
# load the most current version of GNU parallel
module load tools/parallel/20190822
#module load lang/Python/3.6.4-foss-2018a
module load lang/Python/3.7.4-GCCcore-8.3.0
module load bio/Biopython/1.74-foss-2019a
#TODO: find a solution for the bug in BLAST+ AND to select the version by hand
module load bio/BLAST+/2.9.0-gompi-2019a
#module load bio/BLAST+/2.7.1-foss-2018a
......@@ -446,7 +445,7 @@ done
### get query and database files
FASTA=$_arg_fasta
DATABASE=$_arg_database
DATABASE=$(realpath $_arg_database)
### check if query & database exist
if [[ $_arg_test == "off" ]] && [ ! -e "$FASTA" ]; then
......@@ -641,7 +640,7 @@ nentries=$(grep '>' $FASTA | wc -l)
### check if this script is on node by checking env-variable $SLURM_JOB_ID, else send it to SLURM with given parameters and exit
if [ -z "$SLURM_JOB_ID" ]; then
export SCRIPT_PATH=$(dirname $0)
submit_statement="sbatch --no-requeue -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"
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 $DATABASE"
if [ -n "$_arg_reservation" ]; then
......@@ -714,7 +713,6 @@ if [ ! -d "$WORKDIR/$SPLITFILEDIR" ]; then
mkdir -p "$WORKDIR/$SPLITFILEDIR" || exit 1;
mkdir -p "$WORKDIR/output" || exit 1;
cd "$WORKDIR"
pip install biopython
echo "executing scratch generator on $FASTA ($_arg_splitup_per_queryfile entries per file)"
eval "${SCRIPT_PATH}/splitter.py $FASTA $_arg_splitup_per_queryfile " & # splitup queryfile
queue $!
......