--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mlmm/MLMM.sh	Thu Jul 02 05:42:38 2015 -0400
@@ -0,0 +1,28 @@
+#!/bin/bash
+geno=$1
+map=$2
+pheno=$3
+steps=$4
+method=$5
+output=$6
+pdf=$7
+kinship=$8
+rss=$9
+step_table=${10}
+log=${11}
+
+directory=`dirname $0`
+mkdir tmpdir$$
+cp -rf $geno tmpdir$$/geno
+cp -rf $map tmpdir$$/map
+cp -rf $pheno tmpdir$$/pheno
+ 
+perl $directory/MLMM.pl -g tmpdir$$/geno -i tmpdir$$/map -p tmpdir$$/pheno -s $steps -m $method -o tmpdir$$/output -d $directory/source_library >>$log 2>&1
+
+mv tmpdir$$/output.pdf $pdf
+mv tmpdir$$/output.kinship $kinship
+mv tmpdir$$/output.res_asso $output
+mv tmpdir$$/output.rss $rss
+mv tmpdir$$/output.steptable $step_table
+
+