Mercurial > repos > jjohnson > snpeff_with_dep

diff snpEff_download.xml @ 14:ef4598ea7179

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Add SnpSift dependency
author Jim Johnson <jj@umn.edu>
date Fri, 21 Sep 2012 16:00:25 -0500
parents e9e4ff80e72b
children aab5e0adb26d
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--- a/snpEff_download.xml	Fri Sep 21 15:16:49 2012 -0500
+++ b/snpEff_download.xml	Fri Sep 21 16:00:25 2012 -0500
@@ -4,7 +4,7 @@
 		<requirement type="package" version="3.0">snpEff</requirement>
 		<requirement type="set_environment">JAVA_JAR_PATH </requirement>
 	</requirements>
-	<command>java -jar $JAVA_JAR_PATH/snpEff.jar download -c $JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
+	<command>java -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
 	<inputs>
 		<param name="genomeVersion" type="select" label="Genome">
 				<option value="ailmel1.61">Ailuropoda melanoleuca : ailmel1.61</option>