Mercurial > repos > jorrit > obotest
view tool_dependencies.xml @ 2:e71204d5e03c draft
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author | jorrit |
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date | Thu, 07 Feb 2013 16:57:42 -0500 |
parents | 569830319099 |
children | 0c42bebab126 |
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<?xml version="1.0"?> <tool_dependency> <package name="freebayes" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf"> <install version="1.0"> <actions> <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action> <action type="shell_command">git checkout 9608597d12e127c847ae03aa03440ab63992fedf</action> <action type="shell_command">git submodule update --recursive</action> <action type="shell_command">make</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> FreeBayes requires g++ and the standard C and C++ development libraries. Additionally, cmake is required for building the BamTools API. </readme> </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> </package> </tool_dependency>