Patch a bug to launch exonerate on complexe filename

Former-commit-id: e8357a639a22cb123985a0ed487dfd4018c9bb0a
Former-commit-id: a2e1c2ce75c0eac9574b7a68506f6f209e54ea89

detectors/cds/bin/do_exonerate.csh

@@ -110,8 +110,21 @@ set base = $OutDir/$GenoName.$ProtName
 #
 # Alias the genome filename to a short name 
 # to circumvent a bug in exonerate 
-set ShortLink = $OutDir/genome.fasta
-ln -s $GenoFile $ShortLink
+
+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 ShortDir  = `mktemp -d`
+set ShortLink = $ShortDir/genome.fasta
+ln -s $AbsGenoFile $ShortLink
+Notify "  Building input shortcut $AbsGenoFile --> $ShortLink"
 
 #
 # skip exonerate calculations if already done
@@ -232,7 +245,8 @@ $AwkCmd -f $LIB_DIR/toEmbl.awk $base.iff |\
 # end
 #
 
-rm -f $ShortLink
+rm -rf $ShortDir
+
 Notify "  output file: $base.res"
 
 (\rm -f ?_$$) >> /dev/null

detectors/cds/bin/go_cds.csh

@@ -63,6 +63,8 @@ foreach dir ("core" "shell" "dust")
   endif
 end
 
+cp $temp/ $Genome.cds.fasta $Genome.cds.fasta 
+
 #
 # pass2: transsplicing
 #
@@ -71,6 +73,8 @@ end
 # pass3: prokov
 #
 
+$PROG_DIR/do_prokov.sh $Fasta $Genome.cds.fasta $temp
+
 #
 # end : output on stdout
 #