PhyloSkims/annotate
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call explicitely tcsh to workaround a path bug

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Former-commit-id: e6c05a695a6872dd5fb8acd96ee031844dd21fa0
Former-commit-id: 7740135e0861b796e85fce0c9c62a4793f836c2b
This commit is contained in:
Eric Coissac
2016-04-13 17:32:10 +02:00
parent f466f5505a
commit 536a451510
3 changed files with 5 additions and 4 deletions
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2
detectors/cds/bin/do_exonerate.sh
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@ -122,7 +122,7 @@ endif
if ($PASS1_SPEEDUP != 0) then if ($PASS1_SPEEDUP != 0) then
$PROG_DIR/do_filterbx.sh $GenoFile $ProtFile \ tcsh -f $PROG_DIR/do_filterbx.sh $GenoFile $ProtFile \
$PASS1_BLASTX_FILTER_IDMIN \ $PASS1_BLASTX_FILTER_IDMIN \
$PASS1_BLASTX_FILTER_NBMIN \ $PASS1_BLASTX_FILTER_NBMIN \
$PASS1_BLASTX_FILTER_NBMAX > D_$$ $PASS1_BLASTX_FILTER_NBMAX > D_$$

2
detectors/cds/bin/go_cds.sh
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@ -58,7 +58,7 @@ foreach dir ("core" "shell" "dust")
set fams = `ls $DbRoot/$dir/*.fst` set fams = `ls $DbRoot/$dir/*.fst`
Notify "running pass1:$dir exonerate of $Genome on $DbRoot" Notify "running pass1:$dir exonerate of $Genome on $DbRoot"
foreach f ($fams) foreach f ($fams)
$PROG_DIR/do_exonerate.sh $Fasta $f $DbRoot/models $temp tcsh -f $PROG_DIR/do_exonerate.sh $Fasta $f $DbRoot/models $temp
end end
endif endif
end end

5
org-annotate.sh
View File

@ -14,6 +14,7 @@
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"
# #
# Management of options # Management of options
# #
@ -95,10 +96,10 @@ pushTmpDir ORG.organnot
loginfo "Done." loginfo "Done."
loginfo "Annotating the CDS..." loginfo "Annotating the CDS..."
${PROG_DIR}/detectors/cds/bin/go_cds.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot" tcsh -f ${PROG_DIR}/detectors/cds/bin/go_cds.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done." loginfo "Done."
loginfo "Printing minimal header..." loginfo "Printing minimal header..."
echo "ID XXX; XXX; circular; genomic DNA; XXX; XXX; $(seqlength ${RESULTS}.norm.fasta) BP." echo "ID XXX; XXX; circular; genomic DNA; XXX; XXX; $(seqlength ${RESULTS}.norm.fasta) BP."
echo "XX" echo "XX"
echo "AC XXX;" echo "AC XXX;"