Mercurial > repos > fcaramia > jointsnvmix
view tool_dependencies.xml @ 2:26953f1c8af2 draft default tip
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author | fcaramia |
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date | Thu, 20 Jun 2013 00:53:38 -0400 |
parents | 7fb20f2d156c |
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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">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> Compiling SAMtools requires the ncurses and zlib development libraries. </readme> </package> <package name="cython" version="0.19.1"> <install version="1.0"> <actions> <action type="download_by_url">http://cython.org/release/Cython-0.19.1.tar.gz</action> <action type="make_directory">$INSTALL_DIR/lib/python</action> <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> <action type="set_environment"> <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> </readme> </package> <package name="pysam" version="0.5"> <install version="1.0"> <actions> <action type="download_by_url">http://pysam.googlecode.com/files/pysam-0.5.tar.gz</action> <action type="make_directory">$INSTALL_DIR/lib/python</action> <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> <action type="set_environment"> <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> </action> </actions> </install> <readme> </readme> </package> <package name="jointsnvmix" version="0.7.5"> <install version="1.0"> <actions> <action type="download_by_url">http://joint-snv-mix.googlecode.com/files/JointSNVMix-0.7.5.tar.gz</action> <action type="make_directory">$INSTALL_DIR/lib/python</action> <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> <action type="set_environment"> <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> jointsnvmix requires python 2.7 </readme> </package> </tool_dependency>