From 8d2ec19fe8b8de3fe162a10aa806fb192421aa03 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Wed, 24 Jan 2018 14:30:00 +0100
Subject: [PATCH] Patch a bug to launch exonerate on complexe filename

Former-commit-id: e8357a639a22cb123985a0ed487dfd4018c9bb0a
Former-commit-id: a2e1c2ce75c0eac9574b7a68506f6f209e54ea89
---
 detectors/cds/bin/do_exonerate.csh | 20 +++++++++++++++++---
 detectors/cds/bin/go_cds.csh       |  4 ++++
 2 files changed, 21 insertions(+), 3 deletions(-)

diff --git a/detectors/cds/bin/do_exonerate.csh b/detectors/cds/bin/do_exonerate.csh
index 316299e..9962ebb 100755
--- a/detectors/cds/bin/do_exonerate.csh
+++ b/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
diff --git a/detectors/cds/bin/go_cds.csh b/detectors/cds/bin/go_cds.csh
index 78f42dc..14b3591 100755
--- a/detectors/cds/bin/go_cds.csh
+++ b/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
 #