view tool_dependencies.xml @ 68:bc398d6bac85 draft

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<?xml version="1.0"?>
<tool_dependency>
	
	<package name="ncurses" version="5.9">
		<repository changeset_revision="f62fa47b852d" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
	</package>
	
	<!-- Optimized samtools (for threaded mpileup) -->
	<package name="samtools_parallel_mpileup" version="0.1.19">
		<install version="1.0">
			<actions>
				<action type="set_environment_for_install">
					<repository changeset_revision="f62fa47b852d" name="package_ncurses_5_9" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
						<package name="ncurses" version="5.9" />
					</repository>
				</action>
				<action type="shell_command">svn checkout https://github.com/yhoogstrate/parallel-mpileup/trunk samtools-parallel-mpileup &amp;&amp; cd samtools-parallel-mpileup</action>
				<action type="shell_command">sed -i 's/-lcurses/-lncurses/' Makefile</action>
				<action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action>
				<action type="shell_command">cd samtools-parallel-mpileup &amp;&amp; cd $(ls |grep samtools-) &amp;&amp; make &amp;&amp; cp samtools ../samtools-parallel-mpileup</action>
				<action type="move_file">
					<source>samtools-parallel-mpileup</source>
					<destination>$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 a modified version of samtools, able to paralellize the mpileup function.
		</readme>
	</package>
	
	<package name="package_samtools_0_1_19" version="0.1.19">
		<repository changeset_revision="40250a414486" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
	</package>
	
	<package name="varscan" version="2.3.6">
		<repository changeset_revision="f82940004c84" name="varscan_version_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
	</package>
</tool_dependency>