Mercurial > repos > fcaramia > contra
view tool_dependencies.xml @ 23:2770f49cb0dc
re-uploading contra
author | Franco Caramia <franco.caramia@petermac.org> |
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date | Tue, 20 May 2014 09:59:00 +1000 |
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children | c361b3fb806e |
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<?xml version="1.0"?> <tool_dependency> <package name="samtools" version="0.1.18"> <install version="1.0"> <actions> <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action> <action type="shell_command">make</action> <action type="move_file"> <source>samtools</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="move_file"> <source>misc/maq2sam-long</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> Compiling SAMtools requires the ncurses and zlib development libraries. </readme> </package> <package name="bedtools" version="2.17.0"> <install version="1.0"> <actions> <action type="download_by_url" target_filename="bedtools-2.17.0.tar.gz" >http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz</action> <action type="shell_command">make all</action> <action type="make_directory">$INSTALL_DIR/bin</action> <action type="move_directory_files"> <source_directory>bin</source_directory> <destination_directory>$INSTALL_DIR/bin</destination_directory> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools. g++ required </readme> </package> <package name="contra" version="2.0.4"> <install version="1.0"> <actions> <action type="download_by_url">http://downloads.sourceforge.net/project/contra-cnv/CONTRA.V2.0/CONTRA.v2.0.4.tar.gz</action> <action type="shell_command">rm -rf bedtools_installation_guide.txt</action> <action type="shell_command">rm -rf BEDTools-User-Manual.v4.pdf</action> <action type="shell_command">rm -rf BEDTools.v2.11.2.tar.gz</action> <action type="shell_command">rm -rf CONTRA_User_Guide.2.0.pdf</action> <action type="make_directory">$INSTALL_DIR/bin</action> <action type="make_directory">$INSTALL_DIR/bin/scripts</action> <action type="move_file"> <source>contra.py</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="move_file"> <source>baseline.py</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="move_directory_files"> <source_directory>scripts</source_directory> <destination_directory>$INSTALL_DIR/bin/scripts</destination_directory> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> Contra requires Samtools, Bedtools, Python and R </readme> </package> </tool_dependency>