Mercurial > repos > jeremie > package_pindel_0_2_5

view tool_dependencies.xml @ 1:7a1b7941a04f draft

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author jeremie
date Wed, 02 Jul 2014 05:25:24 -0400
parents 568c8f5371fc
children 2e7e0d92cb40
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line source

<?xml version="1.0"?>
<tool_dependency>
	<package name="samtools" version="0.1.18">
		<repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.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">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> -->
				<action type="shell_command">./INSTALL $BAM_ROOT/include/bam</action>
				<action type="move_file">
                    <source>pindel</source>
                    <destination>$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>
				</action>
			</actions>
		</install>
		<readme>
		</readme>
	</package>
</tool_dependency>