Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam

changeset 33:3f62f407068e

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Uploaded
author yhoogstrate
date Tue, 18 Feb 2014 05:29:50 -0500
parents 2b6a44353622
children 7946b09020e0
files tool_dependencies.xml
diffstat 1 files changed, 4 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Mon Feb 17 10:47:38 2014 -0500
+++ b/tool_dependencies.xml	Tue Feb 18 05:29:50 2014 -0500
@@ -21,14 +21,13 @@
 	<package name="VarScan" version="2.3.6">
 		<install version="1.0">
 			<actions>
-				<action type="shell_command">wget http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar --output-file="VarScan.v2.3.6.jar"</action>
+				<action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action>
 				<action type="move_file">
-					<source>../VarScan.v2.3.6.jar</source>
-					<destination>$INSTALL_DIR/bin</destination>
+					<source>VarScan.v2.3.6.jar</source>
+					<destination>$INSTALL_DIR/jars</destination>
 				</action>
 				<action type="set_environment">
-					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-					<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+					<environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
 				</action>
 			</actions>
 		</install>