--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/igblast/igblast.sh	Thu Jul 30 09:31:38 2015 -0400
@@ -0,0 +1,15 @@
+set -e
+
+dir="$(cd "$(dirname "$0")" && pwd)"
+
+input=$1
+species=$2
+locus=$3
+output=$4
+
+
+echo "$input $species $locus $output"
+
+java -jar igblastwrp.jar -cf -S $species -R $locus ${input} $PWD/blasted_output
+
+Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1