From 536a451510099e150b6a7a583c176f4d7fdfd2ea Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Wed, 13 Apr 2016 17:32:10 +0200
Subject: [PATCH] call explicitely tcsh to workaround a path bug

Former-commit-id: e6c05a695a6872dd5fb8acd96ee031844dd21fa0
Former-commit-id: 7740135e0861b796e85fce0c9c62a4793f836c2b
---
 detectors/cds/bin/do_exonerate.sh | 2 +-
 detectors/cds/bin/go_cds.sh       | 2 +-
 org-annotate.sh                   | 5 +++--
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/detectors/cds/bin/do_exonerate.sh b/detectors/cds/bin/do_exonerate.sh
index 78b6898..e0511ab 100755
--- a/detectors/cds/bin/do_exonerate.sh
+++ b/detectors/cds/bin/do_exonerate.sh
@@ -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_$$
diff --git a/detectors/cds/bin/go_cds.sh b/detectors/cds/bin/go_cds.sh
index 6561a90..c8ed8e2 100755
--- a/detectors/cds/bin/go_cds.sh
+++ b/detectors/cds/bin/go_cds.sh
@@ -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 $temp
     end
   endif
 end
diff --git a/org-annotate.sh b/org-annotate.sh
index bf7e088..03ad117 100755
--- a/org-annotate.sh
+++ b/org-annotate.sh
@@ -14,6 +14,7 @@
 THIS_DIR="$(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;"