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Detect number of cores

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This commit is contained in:
Eric Coissac
2025-05-24 08:46:13 +02:00
parent 534c5c74a8
commit c5b92799b1
2 changed files with 8 additions and 2 deletions
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data/cds/sp_chlorodb/.DS_Store vendored
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10
detectors/cds/bin/go_cds.sh
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@ -22,6 +22,12 @@
THIS_DIR="$(dirname ${BASH_SOURCE[0]})" THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source "${THIS_DIR}/../../../scripts/bash_init.sh" source "${THIS_DIR}/../../../scripts/bash_init.sh"
if [[ -z "$ANNOT_MAXCPU" ]] ; then
Threads=$(nproc)
else
Threads=$ANNOT_MAXCPU
fi
needarg 1 needarg 1
Fasta=$1; shift Fasta=$1; shift
@ -74,7 +80,7 @@ if [[ "$cdsdetection_pass1" == "yes" ]] ; then
echo tcsh -f $PROG_DIR/do_exonerate.csh Pass1 $Fasta $f $AnnotFile $DbRoot/models $temp echo tcsh -f $PROG_DIR/do_exonerate.csh Pass1 $Fasta $f $AnnotFile $DbRoot/models $temp
done done
fi fi
done ) | parallel -j 8 done ) | parallel -j $Threads
mv $temp/genome.cds.fasta $Genome.cds_pass1.fasta mv $temp/genome.cds.fasta $Genome.cds_pass1.fasta
fi fi
@ -103,7 +109,7 @@ if [[ "$cdsdetection_pass3" == "yes" ]] ; then
echo tcsh -f $PROG_DIR/do_exonerate.csh Pass3 $Fasta $f $AnnotFile $DbRoot/models $temp echo tcsh -f $PROG_DIR/do_exonerate.csh Pass3 $Fasta $f $AnnotFile $DbRoot/models $temp
done done
fi fi
done) | parallel -j 8 done) | parallel -j $Threads
mv $temp/genome.cds.fasta $Genome.cds_pass2.fasta mv $temp/genome.cds.fasta $Genome.cds_pass2.fasta
fi fi