diff --git a/detectors/cds/bin/go_cds.csh b/detectors/cds/bin/go_cds.csh
deleted file mode 100755
index 31390dd..0000000
--- a/detectors/cds/bin/go_cds.csh
+++ /dev/null
@@ -1,115 +0,0 @@
-#!/usr/bin/env tcsh -f
-#
-#                           Annotate CDS 
-#
-#========================================================================================
-#
-#  Annotate CDS
-#
-#  go_cds.sh <FASTAFILE>
-#
-#		- <FASTAFILE> : The fasta file containing the genome to annotate
-#
-#  Results are printed to the standard output
-#
-#========================================================================================
-# usage: go_cds.sh fasta [db_root]
-#
-unsetenv ORG_SOURCED
-
-setenv ORG_HOME `dirname $0`/../../..
-source $ORG_HOME/scripts/csh_init.sh
-
-NeedArg 1
-
-set Fasta = $Argv[1]; Shift
-
-NeedFile $Fasta
-
-set Genome = `basename $Fasta:r`
-
-set DbRoot = $CDS_DATA_DIR/chlorodb
-
-if ($#Argv > 0) then
-  set DbRoot = $Argv[1]; Shift
-endif
-
-NeedDir $DbRoot/core
-NeedFile $DbRoot/core/Annot.lst
-
-NeedDir $DbRoot/models
-
-#
-# run everything into temporary place
-#
-
-set temp = `hostname`.$$.Genome.tmp
-if (! -d $temp) then
-  Notify "making directory $temp"
-  mkdir $temp
-endif
-
-#
-# find the absolute path of the fasta genome file
-#
-echo $Fasta | grep '^/' > /dev/null
-if ( $status == 1 ) then
-	set AbsGenoFile = `pwd`/$Fasta
-	set DirGenoFile = `dirname $AbsGenoFile`
-	set DirGenoFile = `(cd $DirGenoFile;pwd)`
-	set AbsGenoFile = $DirGenoFile/`basename $AbsGenoFile`
-else
-	set AbsGenoFile = $Fasta
-endif
-
-pushd $temp >& /dev/null
-ln -s $AbsGenoFile genome.fasta
-popd >& /dev/null
-
-set Fasta = $temp/genome.fasta
-
-
-#
-# pass1: run exonerate
-#
-
-foreach dir ("core" "shell" "dust")
-  if (-d $DbRoot/$dir) then
-    set fams = `ls $DbRoot/$dir/*.clean.fst`
-    Notify "running pass1:$dir exonerate of $Genome on $DbRoot"
-    foreach f ($fams)
-      tcsh -f $PROG_DIR/do_exonerate.csh $Fasta $f $DbRoot/models $temp
-    end
-  endif
-end
-
-cp $temp/genome.cds.fasta $Genome.cds.fasta 
-
-#
-# pass2: transsplicing
-#
-
-$PROG_DIR/do_rps12.sh $Fasta > $temp/$Genome.rps12.res
-
-#
-# pass3: prokov
-#
-
-# $PROG_DIR/do_prokov.sh $Fasta $Genome.cds.fasta $temp
-
-#
-# end : output on stdout
-#
-
-cat $temp/*.res
-
-# cleanup everything
-
-AssignUndef TMP_CLEANUP 1
-
-if ($TMP_CLEANUP != 0) then
-  Notify "  cleanup $temp"
-  (\rm -r $temp) >& /dev/null
-endif
-
-Exit 0
diff --git a/detectors/cds/bin/go_cds.sh b/detectors/cds/bin/go_cds.sh
new file mode 100755
index 0000000..014266f
--- /dev/null
+++ b/detectors/cds/bin/go_cds.sh
@@ -0,0 +1,110 @@
+#!/bin/bash
+#
+#                           Annotate CDS 
+#
+#========================================================================================
+#
+#  Annotate CDS
+#
+#  go_cds.sh <FASTAFILE> [DBROOT]
+#
+#		- <FASTAFILE> : The fasta file containing the genome to annotate
+#       - [DBROOT]    : optionnal argument allowing to specify database directory
+#
+#  Results are printed to the standard output
+#
+#========================================================================================
+# usage: go_cds.sh fasta [db_root]
+#
+
+# -- CAUTION -- Works as long than the script 
+#               is not called through a symlink
+THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
+source "${THIS_DIR}/../../../scripts/bash_init.sh"
+
+needarg 1
+
+Fasta=$1; shift
+
+needfile $Fasta
+
+# Genome names is set from the base
+# name of the genome file without its extension
+Genome=$(basename ${Fasta%.*})
+
+# DbRoot is set to its default values except 
+# if the second argument precise another DbRoot
+
+DbRoot="$CDS_DATA_DIR/chlorodb"
+
+if (( $# > 0)) ; then
+  DbRoot="$1"; Shift
+fi
+
+needdir $DbRoot
+needdir $DbRoot/core
+needfile $DbRoot/core/Annot.lst
+needdir $DbRoot/models
+
+assignundef cdsdetection_pass1 yes
+assignundef cdsdetection_pass2 yes
+
+temp=$(mktempdir $(hostname))
+
+AbsGenoFile=$(getAbsolutePath $Fasta)
+pushd $temp >& /dev/null
+ln -s $AbsGenoFile genome.fasta
+popd >& /dev/null
+
+Fasta="$temp/genome.fasta"
+
+#
+# pass1: run exonerate
+#
+
+if [[ "$cdsdetection_pass1" == "yes" ]] ; then
+    for dir in "core" "shell" "dust" ; do
+    if [[ -d $DbRoot/$dir ]] ; then
+        fams=$(ls $DbRoot/$dir/*.clean.fst)
+        loginfo "running pass1:$dir exonerate of $Genome on $DbRoot"
+        for f in $fams ; do
+        tcsh -f $PROG_DIR/do_exonerate.csh $Fasta $f $DbRoot/models $temp
+        done
+    fi
+    done
+
+    cp $temp/genome.cds.fasta $Genome.cds.fasta 
+
+fi
+
+
+#
+# pass2: transsplicing
+#
+
+if [[ "$cdsdetection_pass2" == "yes" ]] ; then
+    $PROG_DIR/do_rps12.sh $Fasta $temp
+fi
+
+#
+# pass3: prokov
+#
+
+# $PROG_DIR/do_prokov.sh $Fasta $Genome.cds.fasta $temp
+
+#
+# end : output on stdout
+#
+
+cat $temp/*.res
+
+# cleanup everything
+
+assignundef TMP_CLEANUP 1
+
+if (( $TMP_CLEANUP != 0 )) ; then
+  loginfo "  cleanup $temp"
+  (\rm -r $temp) >& /dev/null
+fi
+
+exit 0
diff --git a/scripts/bash_init.sh b/scripts/bash_init.sh
index 4b00826..0b5941e 100644
--- a/scripts/bash_init.sh
+++ b/scripts/bash_init.sh
@@ -25,8 +25,16 @@ function getAbsolutePath {
 
 # Manage temp directory
 
-function pushTmpDir {
+function mktempdir {
+	local TMP_DIR
 	TMP_DIR=$(mktemp -d -t "$1_proc_$$_XXXXXX")
+	logdebug "Creating temp directory $TMP_DIR"
+	echo $TMP_DIR
+}
+
+function pushTmpDir {
+	local TMP_DIR
+	TMP_DIR=$(mktempdir "$1")
 	pushd $TMP_DIR >& /dev/null
 	TMP_DIR_STACK="$TMP_DIR $TMP_DIR_STACK"
 	logdebug "Pushing temp directory $TMP_DIR"
@@ -34,8 +42,9 @@ function pushTmpDir {
 }
 
 function popTmpDir {
-	TMP_DIR=$(echo $TMP_DIR_STACK | $AwkCmd '{print $1}')
-	TMP_DIR_STACK=$(echo $TMP_DIR_STACK | $AwkCmd '{$1="";print $0}')
+	local TMP_DIR
+	TMP_DIR=$($AwkCmd '{print $1}' <<< $TMP_DIR_STACK)
+	TMP_DIR_STACK=$($AwkCmd '{$1="";print $0}' <<< $TMP_DIR_STACK)
 	popd  >& /dev/null
 	rm -rf $TMP_DIR >& /dev/null
 	logdebug "Poping temp directory $TMP_DIR"
@@ -86,6 +95,42 @@ function logdebug {
 	fi
 }
 
+# 
+# Asserts that the number of arguments passed to the script
+# is at least equal to the first argument of the function.
+#
+# needarg 3
+#
+# requires that the script is called at least with 3 arguments
+#
+__ORG_ANNOT_ARGS_SCRIPT_COUNT__=$#
+function needarg {
+	if (( $__ORG_ANNOT_ARGS_SCRIPT_COUNT__ < $1 )) ; then
+	    logerror "not enougth arguments provided"
+		exit 1
+	fi
+}
+
+function needfile {
+	if [[ ! -e $1 ]] ; then 
+		logerror "File $1 doesn't exist"
+		exit 1
+	fi
+}
+
+function needdir {
+	if [[ ! -d $1 ]] ; then 
+		logerror "Directory $1 doesn't exist"
+		exit 1
+	fi
+}
+function assignundef {
+    local value=$(eval echo \${$1+x})
+    if [[ -z "$value" ]] ; then 
+       eval $1=$2
+    fi
+}
+
 # Sequence related functions	
 	
 # Counts how many sequences are stored in a fasta file