diff crac_wrapper.sh @ 3:4cf2808854bc draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/crac_wrapper.sh	Fri Sep 13 10:01:00 2013 -0400
@@ -0,0 +1,37 @@
+#!/bin/sh
+
+# Recovering special parameters from crac.xml
+###############################################################
+CRAC_BINARY=crac
+INDEX_INPUT="$1"
+
+# Getting the indexed genome value
+###############################################################
+# Getting the indexed Genome name without the extension
+if [ -d "$INDEX_INPUT" ]; then				# If $INDEX_INPUT is a directory (that is to say an index from the history)
+  cpt=0
+  for fichier in $INDEX_INPUT/*.ssa
+    do
+      if [ $((++cpt)) -gt 1 ]; then 			#More than 1 '.ssa' file is not expected
+        echo "Warning:Multiple indexes found [$INDEX]" >&2
+      fi
+    INDEX=${fichier%%.ssa}				#Getting the index from history
+    done
+  else
+    INDEX="$INDEX_INPUT"				#Getting the prebuilt index
+fi
+if [ ! -f "$INDEX.ssa" -a ! -f "$INDEX.conf" ]; then	#Both '.ssa' and '.conf' files are required
+  echo "Error:Index not found [$INDEX]" >&2
+  exit 1
+fi
+
+# Execution of the command line (Submiting job to the cluster)
+###############################################################
+shift 2					#Avoiding index_input and output_name.extra_files_path
+
+CRAC_CMD_LINE=""$CRAC_BINARY" -i "$INDEX" "$@""
+
+out=`$CRAC_CMD_LINE`
+
+exit 0
+