From 2e5bdf2246398f53d9212bcb62a7abb09749426a 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: fd381611fc7ec543f374e8c6132d29c66612f1a4
Former-commit-id: 653603e547c675c80ace6a3a9d0f13be89048017
---
 detectors/cds/bin/do_exonerate.csh | 15 ++++++++++++++-
 detectors/cds/bin/go_cds.csh       |  4 ++++
 2 files changed, 18 insertions(+), 1 deletion(-)

diff --git a/detectors/cds/bin/do_exonerate.csh b/detectors/cds/bin/do_exonerate.csh
index 316299e..1134eda 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 
+
+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
-ln -s $GenoFile $ShortLink
+ln -s $AbsGenoFile $ShortLink
+Notify "  Building input shortcut $AbsGenoFile --> $ShortLink"
+ls -l $ShortLink
 
 #
 # skip exonerate calculations if already done
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
 #