# HG changeset patch
# User jeremie
# Date 1404468386 14400
# Node ID b5ae2adce876be4ca7ea811844169e64324e18a9
# Parent  b68c61d5e995a38e582f2a9cebe9ec2cd3d6cbb2
Uploaded

diff -r b68c61d5e995 -r b5ae2adce876 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jul 02 06:23:08 2014 -0400
+++ b/tool_dependencies.xml	Fri Jul 04 06:06:26 2014 -0400
@@ -9,50 +9,19 @@
 				<action type="shell_command">git clone https://github.com/genome/pindel.git</action>
 				<action type="shell_command">git checkout tags/v0.2.5</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> -->
+					<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="make_directory">samtools</action>
-				<action type="shell_command">
-					cp $BAM_ROOT/bin/* samtools
-                </action>
-                <action type="shell_command">
-					cp $BAM_ROOT/lib/* samtools
-                </action>
-                <action type="shell_command">
-					cp $BAM_ROOT/include/bam/* samtools
-                </action>
-                <action type="shell_command">ls</action>
-                <action type="shell_command">pwd</action>
-
-           <!--      <action type="shell_command">
-                    <source>$BAM_ROOT/lib</source>
-                    <destination>./samtools</destination>
-                </action>
-                <action type="shell_command">
-                    <source_directory>$BAM_ROOT/include/bam</source_directory>
-                    <destination_directory>./samtools</destination_directory>
-                </action>  -->
-
-
+				<action type="shell_command">cp $BAM_ROOT/bin/* samtools</action>
+				<action type="shell_command">cp $BAM_ROOT/lib/* samtools</action>
+				<action type="shell_command">cp $BAM_ROOT/include/bam/* samtools</action>
 				<action type="shell_command">./INSTALL samtools</action>
-				<action type="move_file">
-                    <source>pindel</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>pindel2vcf</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
+				<action type="move_file"><source>pindel</source><destination>$INSTALL_DIR/bin</destination></action>
+				<action type="move_file"><source>pindel2vcf</source><destination>$INSTALL_DIR/bin</destination></action>
 				<action type="set_environment">
-					<environment_variable name="PATH" action="set_to">$INSTALL_DIR/bin</environment_variable>
+					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
 				</action>
 			</actions>
 		</install>