# HG changeset patch
# User davidvanzessen
# Date 1390554295 18000
# Node ID 2f2544607ad6f4a5e45677fb843d474b011dc2a3
# Parent  6364030a16b86f79ccb0472859f396050e66ae3a
Uploaded

diff -r 6364030a16b8 -r 2f2544607ad6 combined.sh
--- a/combined.sh	Fri Jan 24 04:02:33 2014 -0500
+++ b/combined.sh	Fri Jan 24 04:04:55 2014 -0500
@@ -16,7 +16,7 @@
 
 function blastAndParse {
 	echo "<tr><td>Starting blast of sample $3 of patient $2</td></tr>" >> $html
-	echo "$IGDATA/bin/igblastn -germline_db_V $IGDATA/database/human_gl_V -germline_db_J $IGDATA/database/human_gl_J -germline_db_D $IGDATA/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $IGDATA/optional_file/human_gl.aux -show_translation -outfmt 3 > $PWD/$4"
+	echo "igblastn -germline_db_V $PWD/igblastdatabase/database/human_gl_V -germline_db_J $PWD/igblastdatabase/database/human_gl_J -germline_db_D $PWD/igblastdatabase/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $PWD/igblastdatabase/optional_file/human_gl.aux -show_translation -outfmt 3 > $PWD/$4"
 	igblastn -germline_db_V $PWD/igblastdatabase/database/human_gl_V -germline_db_J $PWD/igblastdatabase/database/human_gl_J -germline_db_D $PWD/igblastdatabase/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $PWD/igblastdatabase/optional_file/human_gl.aux -show_translation -outfmt 3 > $PWD/$4
 	echo "<tr><td>Finished blast of sample $3 of patient $2</td></tr>" >> $html