# HG changeset patch
# User jeremie
# Date 1403184322 14400
# Node ID 3f6014ca8e193e5faa772d4ff729afb5c8708641
# Parent  4e8cf8b6b5721b0b6b78bf2862ec5428f5c3b362
Uploaded

diff -r 4e8cf8b6b572 -r 3f6014ca8e19 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jun 19 09:14:25 2014 -0400
+++ b/tool_dependencies.xml	Thu Jun 19 09:25:22 2014 -0400
@@ -6,9 +6,14 @@
 	<package name="pindel" version="0.2.5">
 		<install version="1.0">
 			<actions>
-				<action type="download_by_url">https://github.com/genome/pindel/archive/master.zip</action>
+				<action type="download_by_url" target_filename="pindel-master.zip">https://github.com/genome/pindel/archive/master.zip</action>
+				<action type="shell_command">unzip pindel-master.zip -d pindel</action>
 				<!-- <action type="shell_command">cd pindel</action>
-				<action type="shell_command">make SAMTOOLS=~/samtools</action> -->
+				<action type="shell_command">make SAMTOOLS=~/samtools</action> 
+				<action type="move_file">
+					<source>pindel</source>
+					<destination>$INSTALL_DIR/</destination>
+				</action>-->
 				<action type="set_environment">
 					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
 				</action>