Mercurial > repos > davidvanzessen > argalaxy_tools

diff igblast/igblast.sh @ 8:8cbc1a8d27ae draft

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Uploaded
author davidvanzessen
date Mon, 19 Dec 2016 08:50:31 -0500
parents 54f6756bacb1
children 4d2a8f98a502
line wrap: on
line diff
--- a/igblast/igblast.sh	Fri Dec 16 09:01:40 2016 -0500
+++ b/igblast/igblast.sh	Mon Dec 19 08:50:31 2016 -0500
@@ -15,9 +15,15 @@
 
 species="${speciesdict[$species]}"
 
+if [ "$species" == "" ]
+then
+	>&2 echo "Species not possible with igBLASTn, use IMGT"
+	exit 1
+fi
+
 echo "$input $species $locus $output"
 
-java -Xmx64G -jar $IGBLASTWRP/igblastwrp.jar -p 4 -S $species -R $locus ${input} $PWD/blasted_output 2>&1
+java -Xmx16G -jar $IGBLASTWRP/igblastwrp.jar -p 4 -S $species -R $locus ${input} $PWD/blasted_output 2>&1
 #java -Xmx64G -jar $dir/igblastwrp.jar -p 4 -S $species -R $locus ${input} $PWD/blasted_output 2>&1
 #java -Xmx64G -jar $dir/migmap-1.0.1.jar -p 4 -S "$species" -R $locus ${input} $PWD/blasted_output 2>&1