--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tassel.sh	Thu Nov 02 05:19:30 2017 -0400
@@ -0,0 +1,47 @@
+#!/bin/bash
+
+analyseType=$1;
+out1=$2;
+out2=$3;
+out3=$4;
+log1=$5;
+galaxyOutDir=$6;
+
+version=$(java -version 2>&1 | grep version)
+if [[ ! $version =~ 1.8 ]]; then
+    echo "Java found: $version. Tassel 5.0 requires java 1.8..." >&2
+    exit 1
+fi
+
+mkdir $galaxyOutDir
+
+# Suppression des 6 premiers arguments de la liste des arguments $@
+shift; shift; shift; shift; shift; shift;
+
+
+if [[ $analyseType == glm ]] 
+then
+ run_pipeline.pl $* >> $log1 2>&1
+ mv "$galaxyOutDir/TASSELGLM1.txt" $out1
+ mv "$galaxyOutDir/TASSELGLM2.txt" $out2
+fi
+
+if [[ $analyseType == mlm ]] 
+then
+ run_pipeline.pl $* >> $log1 2>&1
+ mv "$galaxyOutDir/TASSELMLM1.txt" $out1
+ mv "$galaxyOutDir/TASSELMLM2.txt" $out2
+ mv "$galaxyOutDir/TASSELMLM3.txt" $out3
+fi
+
+if [[ $analyseType == ld ]] 
+then
+ run_pipeline.pl $* >> $log1 2>&1
+fi
+
+
+if [[ $analyseType == ck ]]
+then
+ run_pipeline.pl $* >> $log1 2>&1
+ mv "$galaxyOutDir/kinship.txt" $out1
+fi