view tool_dependencies.xml @ 85:ddbaf017720a draft

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<?xml version="1.0"?>
<tool_dependency>
	<!--
	<package name="ncurses" version="5.9">
		<repository name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" />
	</package>
	-->
	
	<package name="ncurses" version="5.9">
		<repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
	</package>
		
	<package name="samtools" version="0.1.19">
		<repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
	</package>
	
	<package name="samtools_parallel_mpileup_0_1_19a" version="0.1.19a">
		<install version="1.0">
			<actions>
				<action type="set_environment_for_install">
					<repository changeset_revision="c0735727b530" name="package_ncurses_5_9" owner="iuc" toolshed="https://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 ;
				
				cd samtools-parallel-mpileup ;
				cd $(ls |grep samtools-) ;
				
				sed -i 's/-lcurses/-lncurses/' Makefile ;
                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 ;
				
				make ;
				cp samtools ../samtools-parallel-mpileup</action>
				<action type="move_file">
					<source>samtools-parallel-mpileup/samtools-parallel-mpileup</source>
					<destination>$INSTALL_DIR/bin</destination>
				</action>
				<action type="set_environment">
					<environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
					<environment_variable action="prepend_to" name="PATH">$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="varscan" version="2.3.6">
		<repository changeset_revision="f82940004c84" name="varscan_version_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
	</package>
</tool_dependency>