Commit 18ad00be authored by Christian Meesters's avatar Christian Meesters

so far so ungood

parent 64b3185a
......@@ -41,7 +41,7 @@ START=$(date +%s.%N)
module purge
# load the most current version of GNU parallel
module load tools/parallel
module load tools/parallel/20190822
#module load lang/Python/3.6.4-foss-2018a
module load lang/Python/3.7.4-GCCcore-8.3.0
......@@ -439,16 +439,6 @@ done
FASTA=$_arg_fasta
DATABASE=$_arg_database
### checking db for integrity
if [ -e ${DATABASE}*.fa ]; then
DBSUFFIX=".fa"
elif [ -e ${DATABASE}*.fasta ]; then
DBSUFFIX=".fasta"
else
error "no file '.fa' or '.fasta' found in ${DATABASE} - unable to proceed reliably"
exit 1
fi
### check if query & database exist
if [[ $_arg_test == "off" ]] && [ ! -e "$FASTA" ]; then
error "FASTA input was: '$FASTA' - no such file!"
......@@ -460,7 +450,6 @@ if [[ $_arg_test == "off" ]] && [ ! -d "$DATABASE" ]; then
exit 1
fi
#TODO: differentiate between blastn,x,p -- for now, all are equal
if [ "blastx" = "${_arg_executable,,}" ]; then
executable="blastx"
threads=2
......@@ -727,10 +716,7 @@ while [[ ! -z "$(echo $QUEUE| tr -d ' ')" ]]; do
sleep 5
done
set -x
ls $RAMDISK/*
DATABASE=$(find $RAMDISK -name "*${DBSUFFIX}" -print -quit)
set +x
#DATABASE=$RAMDISK/db${DBSUFFIX} #/$(basename $DATABASEPATH)
if [[ -z $DATABASE ]]; then
error "Unable to recognize database, please get in touch with hpc@uni-mainz.de"
......
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