view tool_dependencies.xml @ 7:2312bedfe2a3 draft

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<?xml version="1.0"?>
<tool_dependency>
	<package name="featurecounts" version="1.4.4">
		<install version="1.0">
			<actions>
				<action type="shell_command">wget http://sourceforge.net/projects/subread/files/subread-1.4.4/subread-1.4.4-source.tar.gz &amp;&amp; tar -zxvf subread-1.4.4-source.tar.gz &amp;&amp; cd subread-1.4.4-source/src/ &amp;&amp; make -f Makefile.Linux &amp;&amp; cd ../../</action>
				<action type="move_file">
					<source>../subread-1.4.4-source/bin/featureCounts</source>
					<destination>$INSTALL_DIR/bin/</destination>
				</action>
				<action type="set_environment">
					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
					<!--<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>-->
				</action>
			</actions>
		</install>
		<readme>
			Downloads and installs featureCounts; requires WGET, GNU AUTOTOOLS and TAR to be installed.
		</readme>
	</package>
	
	<package name="featurecounts2bed" version="1.0.0">
		<install version="1.0">
			<actions>
				<action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/featurecounts2bed.sh $INSTALL_DIR/bin/</action>
				<action type="chmod">
					<file mode="755">$INSTALL_DIR/bin/featurecounts2bed.sh</file>
				</action>
				<action type="set_environment">
					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
					<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>
				</action>
			</actions>
		</install>
	</package>
</tool_dependency>