# HG changeset patch
# User jeremie
# Date 1403187454 14400
# Node ID aea585951b97043035b389c080d0cb1c9083638c
# Parent  ea5aad66809955af844dbed6935be59e38037d2e
Uploaded

diff -r ea5aad668099 -r aea585951b97 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jun 19 09:50:48 2014 -0400
+++ b/tool_dependencies.xml	Thu Jun 19 10:17:34 2014 -0400
@@ -6,15 +6,19 @@
 	<package name="pindel" version="0.2.5">
 		<install version="1.0">
 			<actions>
-				<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="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="shell_command">ls</action>
+				<action type="shell_command">cd ..</action>
+				<action type="shell_command">ls</action>
 				<!-- <action type="move_directory_files">
 					<source_directory>.</source_directory>
 					<destination_directory>$INSTALL_DIR</destination_directory>
 				</action> -->
 				<!-- <action type="shell_command">unzip pindel-master.zip -d pindel</action>--> -->
-				<!-- <action type="shell_command">cd pindel</action> -->
+				<action type="shell_command">cd master</action>
 				<action type="shell_command">make SAMTOOLS=~/samtools</action> 
+				<action type="shell_command">./INSTALL ~/samtools</action> 
 				<action type="move_file">
 					<source>pindel</source>
 					<destination>$INSTALL_DIR/</destination>