<?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 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">
					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>$INSTALL_DIR/</destination>
				</action>
				<action type="set_environment">
					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
				</action>
			</actions>
		</install>
		<readme>
		</readme>
	</package>
</tool_dependency>