--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GetAllPatterns.R	Mon Jun 16 16:24:00 2014 -0400
@@ -0,0 +1,24 @@
+sink(file="/tmp/none")
+sink("/dev/null")
+options(warn=-1)
+options(echo=F) 
+
+invisible("EBSeq")
+suppressMessages(library("EBSeq"))
+
+args <- commandArgs()
+inputfile <- args[6]
+outputfile <- args[7]
+#PairwisePlots <-args[6]
+
+print(args)
+
+Conds=strsplit(inputfile,split=",")[[1]]
+
+
+Out=GetPatterns(Conds)
+
+
+#write.table(Out,file=outputfile,quote=F,col.names=T,row.names=T,sep = "\t")
+write.table(Out,file=outputfile,quote=F,col.names=NA,row.names=T,sep = "\t")  ##cms - changed on 11/11/13
+