Mercurial > repos > fcaramia > contra
diff 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 |
parents | |
children | c361b3fb806e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue May 20 09:59:00 2014 +1000 @@ -0,0 +1,80 @@ +<?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> + +