Commit e6c05a69 by Eric Coissac

call explicitely tcsh to workaround a path bug

parent 115a1955
......@@ -122,7 +122,7 @@ endif
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_NBMIN \
$PASS1_BLASTX_FILTER_NBMAX > D_$$
......
......@@ -58,7 +58,7 @@ foreach dir ("core" "shell" "dust")
set fams = `ls $DbRoot/$dir/*.fst`
Notify "running pass1:$dir exonerate of $Genome on $DbRoot"
foreach f ($fams)
$PROG_DIR/do_exonerate.sh $Fasta $f $DbRoot/models $temp
tcsh -f $PROG_DIR/do_exonerate.sh $Fasta $f $DbRoot/models $temp
end
endif
end
......
......@@ -14,6 +14,7 @@
THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source "${THIS_DIR}/scripts/bash_init.sh"
#
# Management of options
#
......@@ -95,10 +96,10 @@ pushTmpDir ORG.organnot
loginfo "Done."
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 "Printing minimal header..."
loginfo "Printing minimal header..."
echo "ID XXX; XXX; circular; genomic DNA; XXX; XXX; $(seqlength ${RESULTS}.norm.fasta) BP."
echo "XX"
echo "AC XXX;"
......
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