# HG changeset patch
# User jeremie
# Date 1403189566 14400
# Node ID 72ef990f1acef9dbab3b12db35e7750c450b6e70
# Parent  6ae878251e83f678eabf270cccd1a3bdf0e86562
Uploaded

diff -r 6ae878251e83 -r 72ef990f1ace tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jun 19 10:43:24 2014 -0400
+++ b/tool_dependencies.xml	Thu Jun 19 10:52:46 2014 -0400
@@ -8,7 +8,8 @@
 			<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">ls</action>
+				<!-- <action type="shell_command">ls</action> -->
+
 				<!-- <action type="shell_command">cd ..</action>
 				<action type="shell_command">ls</action> -->
 				<!-- <action type="move_directory_files">
@@ -17,6 +18,7 @@
 				</action>
 				<action type="shell_command">unzip pindel-master.zip -d pindel</action>
 				<action type="shell_command">cd master</action> -->
+				<action type="shell_command">make Makefile.local</action>
 				<action type="shell_command">make all SAMTOOLS=~/samtools THREADS=2</action>
 				<!-- <action type="shell_command">./INSTALL ~/samtools</action>  -->
 				<action type="move_file">