Mercurial > repos > davidvanzessen > igblastn_immunerepertoire_igg

changeset 2:364b169ffb30 draft

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Uploaded
author davidvanzessen
date Thu, 23 Jan 2014 08:30:59 -0500
parents 7b0d9c107680
children 6364030a16b8
files combined.sh
diffstat 1 files changed, 1 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/combined.sh	Thu Jan 23 08:29:40 2014 -0500
+++ b/combined.sh	Thu Jan 23 08:30:59 2014 -0500
@@ -20,7 +20,7 @@
 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"
-	$IGDATA/bin/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
 
 	echo "<tr><td>Starting parse of sample $3 of patient $2</td></tr>" >> $html