# HG changeset patch
# User jeremie
# Date 1404221454 14400
# Node ID 04a20abab8c267a3af214a96766e7d29aafd4895
# Parent  e1f5cb956f17de9c94d30399781ef1e718155850
Uploaded

diff -r e1f5cb956f17 -r 04a20abab8c2 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jul 01 09:25:50 2014 -0400
+++ b/tool_dependencies.xml	Tue Jul 01 09:30:54 2014 -0400
@@ -7,17 +7,17 @@
 		<install version="1.0">
 			<actions>
 				<action type="shell_command">git clone https://github.com/genome/pindel.git</action>
-<!-- 				<action type="shell_command">
-					echo "$samtools
-					samtools
-					$PATH
-					$INSTALL_DIR"
-				</action> -->
 				<action type="set_environment_for_install">
                     <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu">
                         <package name="samtools" version="0.1.18" />
                    </repository>
                 </action>
+                <action type="shell_command">
+					echo "$samtools
+					$PATH
+					$INSTALL_DIR
+					$BAM_ROOT"
+				</action>
 				<!-- <action type="shell_command">ls</action> -->
 				<!-- <action type="move_directory_files">
 					<source_directory>.</source_directory>