Add scripts to generate reference DBs for LSC and SSC

Former-commit-id: 77fd69c9687bfc7cfd3305299c7c81d2a9eddada
Former-commit-id: 4d09933673c30d6a9b2b9cc985b33ef23d7a99f4

scripts/bash_init.sh

@@ -0,0 +1,117 @@
+#
+# Bash file to be sourced at the begining of each bash script 
+# for setting up basic variables and functions
+#
+
+########################
+#
+# General usage functions
+#
+#
+
+function getAbsolutePath {
+    [[ -d $1 ]] && { cd "$1"; echo "$(pwd -P)"; } || 
+    { cd "$(dirname "$1")"; echo "$(pwd -P)/$(basename "$1")"; }
+}
+
+# Manage temp directory
+
+function pushTmpDir {
+	TMP_DIR=$(mktemp -d -t "$1_proc_$$_")
+	pushd $TMP_DIR >& /dev/null
+}
+
+function popTmpDir {
+	popd  >& /dev/null
+	rm -rf $TMP_DIR >& /dev/null
+}
+
+# Logging functions
+ 
+
+function errcho {
+	>&2 echo $*
+}
+
+function openLogFile {
+	LOGFILE=$1
+	touch ${LOGFILE}
+}
+
+
+function loginfo {
+    errcho `date +'%Y-%m-%d %H:%M:%S'` "[OA INFO   ] $$ -- $1"
+    if [[ ! -z ${LOGFILE} ]]; then
+          echo `date +'%Y-%m-%d %H:%M:%S'` "[OA INFO   ] $$ -- $1" >> ${LOGFILE}
+    fi
+}
+
+function logerror {
+    errcho `date +'%Y-%m-%d %H:%M:%S'` "[OA ERROR  ] $$ -- $1"
+    if [[ ! -z ${LOGFILE} ]]; then
+          echo `date +'%Y-%m-%d %H:%M:%S'` "[OA ERROR   ] $$ -- $1" >> ${LOGFILE}
+    fi
+}
+
+function logwarning {
+    errcho `date +'%Y-%m-%d %H:%M:%S'` "[OA WARNING] $$ -- $1"
+    if [[ ! -z ${LOGFILE} ]]; then
+          echo `date +'%Y-%m-%d %H:%M:%S'` "[OA WARNING] $$ -- $1" >> ${LOGFILE}
+    fi
+}
+
+# Sequence related functions	
+	
+function fastaCount {
+	grep '^>' $1 | wc -l
+}
+
+#
+#
+########################
+
+
+
+########################
+#
+# Local variable definitions
+#
+#
+
+# The absolute path to the ORG.Annote home direcotory
+ORG_HOME=`getAbsolutePath $(dirname ${BASH_SOURCE[0]})/..`
+
+ 
+ORG_PORTNAME=`${ORG_HOME}/config/guess_port`	# The architecture running the ORG.Annnote instance
+
+PROG_DIR="$(getAbsolutePath $(dirname $0))"		# Directory containing the main script file
+
+DATA_DIR="${ORG_HOME}/data"                     # Directory containing reference data for the annotation
+
+CALL_DIR="$(getAbsolutePath $(pwd))"            # Directory from where the main script is called
+
+
+IR_DATA_DIR="${DATA_DIR}/ir"  				  	# Directory containing data related to the 
+												# Inverted repeat strucuture
+								
+
+#
+#
+########################
+
+
+
+########################
+#
+# Altering the environment
+#
+#
+
+# We alter the path to include the bin dir corresponding to the port
+PATH="${ORG_HOME}/ports/${ORG_PORTNAME}/bin:${PATH}"
+export PATH
+
+# Force to basic international setting for a correction behaviour of AWK on mac with float
+export LANG=C
+export LC_ALL=C
+