Commit 90765be8 authored by Christian Meesters's avatar Christian Meesters

removed the outdated run_blast function

parent ed3b2c3e
......@@ -620,23 +620,6 @@ fi
tmp=$(find $DATABASE -name '*00*hr')
# remove the 2nd suffix
DATABASE=${tmp%.*}
function run_blast() {
cd $(dirname $(realpath $0))
#TODO: check for xml extension
outfname=$(basename ${1%fasta}xml)
tmp_out=$JOBDIR/$outfname
trap "rm -f $tmp_out" EXIT
START_BLAST=$(date +%s.%N)
$BLASTEXE -num_threads $SLURM_CPUS_PER_TASK -db $RAMDISK/$(basename $DATABASE) -query ./$1 $BLASTPARAMS -out $tmp_out
END_BLAST=$(date +%s.%N)
elapsed=$(bc <<< "scale=1; (($END_BLAST-$START_BLAST))/60")
#TODO: enable logging in verbose mode
#echo \"Elapsed: \"$elapsed'
#compress when done
gzip $tmp_out
mv ${tmp_out}.gz ./output/${outfname}.gz
}
#export -f run_blast
cmd=$PWD/cmd_file.sh
......
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