--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create_germlines.sh	Tue May 03 09:52:21 2016 -0400
@@ -0,0 +1,22 @@
+#!/bin/bash
+dir="$(cd "$(dirname "$0")" && pwd)"
+
+input=$1
+type=$2
+cloned=$3
+output=$4
+
+cp $input $PWD/input.tab #file has to have a ".tab" extension
+
+if [ "true" == "$cloned" ] ; then
+	cloned="--cloned"
+else
+	cloned=""
+fi
+
+mkdir $PWD/outdir
+
+#/home/galaxy/anaconda3/bin/python $dir/CreateGermlines.py -d $PWD/input.tab -r $germline --outdir $PWD/outdir --outname output -g $type $cloned
+/data/users/david/anaconda3/bin/python $dir/CreateGermlines.py -d $PWD/input.tab -r $dir/IMGT_Human_IGH[VDJ].fasta --outdir $PWD/outdir --outname output -g $type $cloned
+
+mv $PWD/outdir/output_germ-pass.tab $output