--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/deseq.sh	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,21 @@
+#! /bin/sh
+
+#Arguments :
+#$1=targetFile(the list of files) 
+#$2=with or without header
+#$3=with or without replicates
+#$4=OUT_HTML.html
+#$5=OUT_HTML images directory
+#$6=OUT_complete.xls
+#$7=OUT_up.xls
+#$8=OUT_down.xls
+
+#run example: 
+#bash deseq.sh DESeqTools/targetTest.txt 1 1 testOUT_HTML.html /tmp/ testOUT_complet.xls testOUT_up.xls testOUT_down.xls
+
+#echo $5
+#mkdir -p $5 #First, create the images tmp directory given by Galaxy, -p option can create the parent directory which dosen't exist.
+
+mkdir -p $5
+MY_PATH=`dirname $0` 
+cat $MY_PATH/DESeqTools/anadiffGenes2conds.R | R --slave --args $1 $2 $3 $4 $5 $6 $7 $8 $0 < $MY_PATH/DESeqTools/anadiffGenes2conds.R