Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
view tool_dependencies.xml @ 33:3f62f407068e
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author | yhoogstrate |
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date | Tue, 18 Feb 2014 05:29:50 -0500 |
parents | dc091c635cf0 |
children | 17f10d28dab3 |
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<?xml version="1.0"?> <tool_dependency> <package name="samtools-mpileup-parallel" version="1.0.19"> <install version="1.0"> <actions> <action type="shell_command">svn checkout https://github.com/mydatascience/parallel-mpileup/trunk samtools-mpileup-parallel && cd samtools-mpileup-parallel && cd $(ls |grep samtools-) && make && cp samtools ../samtools-mpileup-parallel</action> <action type="move_file"> <source>samtools-mpileup-parallel</source> <destination>$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="VarScan" version="2.3.6"> <install version="1.0"> <actions> <action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action> <action type="move_file"> <source>VarScan.v2.3.6.jar</source> <destination>$INSTALL_DIR/jars</destination> </action> <action type="set_environment"> <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable> </action> </actions> </install> <readme> Downloads VarScan2. </readme> </package> </tool_dependency>