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switched to git
author nilesh
date Mon, 15 Jul 2013 14:09:29 -0500
parents 6baaaaa1f858
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<?xml version="1.0"?>
<tool_dependency>
	<package name="zlib" version="1.2.8">
        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="zlib" owner="nilesh" changeset_revision="28f618926504" />
    </package>
    <package name="bwa" version="0.7.5a">
    	<install version="1.0">
    		<actions>
    			<action type="set_environment_for_install">
                    <repository changeset_revision="28f618926504" name="zlib" owner="nilesh" toolshed="http://testtoolshed.g2.bx.psu.edu">
                        <package name="zlib" version="1.2.8" />
                   </repository>
                </action>
    			<action type="shell_command">git clone https://github.com/lh3/bwa.git</action>
    			<action type="shell_command">cd ./bwa &amp;&amp; make LIBS="-L$ZLIB_PATH -lm -lz -lpthread"</action>
    			<action type="move_file">
                    <source>bwa/bwa</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
    			<action type="set_environment">
    				<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
    			</action>
    		</actions>
    	</install>
    </package>
    <set_environment version="1.0">
        <environment_variable name="RNASEQCPATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>
</tool_dependency>