Mercurial > repos > fcaramia > contra
diff tool_dependencies.xml @ 25:c361b3fb806e
added Nicola Path 2.0
author | Franco Caramia <franco.caramia@petermac.org> |
---|---|
date | Tue, 03 Jun 2014 17:31:28 +1000 |
parents | 2770f49cb0dc |
children | 0bf826f62f04 |
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--- a/tool_dependencies.xml Mon May 19 20:00:44 2014 -0400 +++ b/tool_dependencies.xml Tue Jun 03 17:31:28 2014 +1000 @@ -1,44 +1,28 @@ <?xml version="1.0"?> <tool_dependency> + + <package name="R" version="3.0.3"> + <repository name="package_r_3_0_3" owner="iuc" /> + </package> + <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">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> - Compiling SAMtools requires the ncurses and zlib development libraries. - </readme> + <repository name="package_samtools_0_1_18" owner="devteam" /> </package> - <package name="bedtools" version="2.17.0"> <install version="1.0"> - <actions> - <action type="download_by_url" target_filename="bedtools-2.17.0.tar.gz" >http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz</action> - <action type="shell_command">make all</action> - <action type="make_directory">$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> + <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">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> </install> <readme> GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools. g++ required @@ -48,13 +32,7 @@ <install version="1.0"> <actions> <action type="download_by_url">http://downloads.sourceforge.net/project/contra-cnv/CONTRA.V2.0/CONTRA.v2.0.4.tar.gz</action> - <action type="shell_command">rm -rf bedtools_installation_guide.txt</action> - <action type="shell_command">rm -rf BEDTools-User-Manual.v4.pdf</action> - <action type="shell_command">rm -rf BEDTools.v2.11.2.tar.gz</action> - <action type="shell_command">rm -rf CONTRA_User_Guide.2.0.pdf</action> - <action type="make_directory">$INSTALL_DIR/bin</action> - <action type="make_directory">$INSTALL_DIR/bin/scripts</action> - <action type="move_file"> + <action type="move_file"> <source>contra.py</source> <destination>$INSTALL_DIR/bin</destination> </action> @@ -62,7 +40,7 @@ <source>baseline.py</source> <destination>$INSTALL_DIR/bin</destination> </action> - <action type="move_directory_files"> + <action type="move_directory_files"> <source_directory>scripts</source_directory> <destination_directory>$INSTALL_DIR/bin/scripts</destination_directory> </action>