# HG changeset patch
# User jeremie
# Date 1404219004 14400
# Node ID d671c9bbb36625f3f8fa99700c5c39f3fd1c63f2

Uploaded

diff -r 000000000000 -r d671c9bbb366 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Jul 01 08:50:04 2014 -0400
@@ -0,0 +1,56 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<package name="samtools" version="0.1.18">
+		<repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" prior_installation_required="True" />
+	</package>
+	<package name="pindel" version="0.2.5">
+		<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
+					$INSTALL_DIR"
+				</action> -->
+				<!-- <action type="shell_command">ls</action> -->
+				<!-- <action type="move_directory_files">
+					<source_directory>.</source_directory>
+					<destination_directory>$INSTALL_DIR</destination_directory>
+				</action>
+				<action type="shell_command">unzip pindel-master.zip -d pindel</action>
+				<action type="shell_command">cd master</action> -->
+				<!-- <action type="shell_command">sed '50d' Makefile</action> -->
+				<!-- <action type="shell_command">make Makefile.local</action> -->
+				<!-- <action type="shell_command">
+				echo "SAMTOOLS=
+				THREADS=
+				COLOUSINGBD15_TIME=60
+				COLOWOBD15_TIME=80
+				SIM1CHRVS20305_TIME=60" > Makefile.local
+				</action>
+				<action type="shell_command">make SAMTOOLS=samtools THREADS=2</action>
+				<action type="move_file">
+					<source>pindel</source>
+					<destination>$INSTALL_DIR/</destination>
+				</action> -->
+				<action type="shell_command">./INSTALL samtools</action>
+
+				<action type="move_file">
+                    <source>pindel</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>pindel2vcf</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+
+				<action type="set_environment">
+					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+				</action>
+			</actions>
+		</install>
+		<readme>
+		</readme>
+	</package>
+</tool_dependency>