Commit fd381611 authored by Eric Coissac's avatar Eric Coissac

Patch a bug to launch exonerate on complexe filename

parent 626566f2
...@@ -110,8 +110,21 @@ set base = $OutDir/$GenoName.$ProtName ...@@ -110,8 +110,21 @@ set base = $OutDir/$GenoName.$ProtName
# #
# Alias the genome filename to a short name # Alias the genome filename to a short name
# to circumvent a bug in exonerate # to circumvent a bug in exonerate
echo $GenoFile | grep '^/' > /dev/null
if ( $status == 1 ) then
set AbsGenoFile = `pwd`/$GenoFile
set DirGenoFile = `dirname $AbsGenoFile`
set DirGenoFile = `(cd $DirGenoFile;pwd)`
set AbsGenoFile = $DirGenoFile/`basename $AbsGenoFile`
else
set AbsGenoFile = $GenoFile
endif
set ShortLink = $OutDir/genome.fasta set ShortLink = $OutDir/genome.fasta
ln -s $GenoFile $ShortLink ln -s $AbsGenoFile $ShortLink
Notify " Building input shortcut $AbsGenoFile --> $ShortLink"
ls -l $ShortLink
# #
# skip exonerate calculations if already done # skip exonerate calculations if already done
......
...@@ -63,6 +63,8 @@ foreach dir ("core" "shell" "dust") ...@@ -63,6 +63,8 @@ foreach dir ("core" "shell" "dust")
endif endif
end end
cp $temp/ $Genome.cds.fasta $Genome.cds.fasta
# #
# pass2: transsplicing # pass2: transsplicing
# #
...@@ -71,6 +73,8 @@ end ...@@ -71,6 +73,8 @@ end
# pass3: prokov # pass3: prokov
# #
$PROG_DIR/do_prokov.sh $Fasta $Genome.cds.fasta $temp
# #
# end : output on stdout # end : output on stdout
# #
......
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