# HG changeset patch
# User jeremie
# Date 1404220909 14400
# Node ID cb62219c677967b0c0d2b79e3689c64b99758bdd
# Parent  cd0aa2ed028d9baf94fe6c5aa5d4803b5dc01325
Uploaded

diff -r cd0aa2ed028d -r cb62219c6779 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jul 01 08:55:05 2014 -0400
+++ b/tool_dependencies.xml	Tue Jul 01 09:21:49 2014 -0400
@@ -7,12 +7,17 @@
 		<install version="1.0">
 			<actions>
 				<action type="shell_command">git clone https://github.com/genome/pindel.git</action>
-				<!-- <action type="shell_command">
+<!-- 				<action type="shell_command">
 					echo "$samtools
 					samtools
 					$PATH
 					$INSTALL_DIR"
 				</action> -->
+				<action type="set_environment_for_install">
+                    <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="samtools" version="0.1.18" />
+                   </repository>
+                </action>
 				<!-- <action type="shell_command">ls</action> -->
 				<!-- <action type="move_directory_files">
 					<source_directory>.</source_directory>
@@ -34,7 +39,7 @@
 					<source>pindel</source>
 					<destination>$INSTALL_DIR/</destination>
 				</action> -->
-				<action type="shell_command">./INSTALL samtools</action>
+				<action type="shell_command">./INSTALL BAM_ROOT</action>
 				<action type="move_file">
                     <source>pindel</source>
                     <destination>$INSTALL_DIR/bin</destination>