# HG changeset patch
# User jeremie
# Date 1403185592 14400
# Node ID 9053dc56c65af86290bbe13e20c5f67221c3cae9
# Parent  c8bdd88ddbbaa82201d01dbbd7775c6fa9f91ff5
Uploaded

diff -r c8bdd88ddbba -r 9053dc56c65a tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jun 19 09:38:22 2014 -0400
+++ b/tool_dependencies.xml	Thu Jun 19 09:46:32 2014 -0400
@@ -6,12 +6,13 @@
 	<package name="pindel" version="0.2.5">
 		<install version="1.0">
 			<actions>
-				<action type="download_by_url" target_filename="pindel-master.zip">https://github.com/genome/pindel/archive/master.zip</action>
-				<action type="move_directory_files">
+				<action type="shell_command">git clone https://github.com/genome/pindel.git pindel</action>
+				<!-- <action type="download_by_url" target_filename="pindel-master.zip">https://github.com/genome/pindel/archive/master.zip</action> -->
+				<!-- <action type="move_directory_files">
 					<source_directory>.</source_directory>
 					<destination_directory>$INSTALL_DIR</destination_directory>
-				</action>
-				<action type="shell_command">unzip pindel-master.zip -d pindel</action>-->
+				</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="move_file">