Mercurial > repos > davidvanzessen > argalaxy_tools

diff igblast/igblast.sh @ 0:afe85eb6572e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Mon, 29 Aug 2016 05:41:20 -0400
parents
children d001d0c05dbe
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/igblast/igblast.sh	Mon Aug 29 05:41:20 2016 -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 -Xmx64G -jar $IGBLASTWRP/igblastwrp.jar -p 4 -S $species -R $locus ${input} $PWD/blasted_output 2>&1
+
+Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1