Mercurial > repos > fcaramia > jointsnvmix
diff tool_dependencies.xml @ 0:a1034918ab9b draft
Uploaded
author | fcaramia |
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date | Thu, 20 Jun 2013 00:03:08 -0400 |
parents | |
children | 7fb20f2d156c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Jun 20 00:03:08 2013 -0400 @@ -0,0 +1,82 @@ +<?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">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + Compiling SAMtools requires the ncurses and zlib development libraries. + </readme> + </package> + + <package name="python" version="2.7"> + <readme> + JointSNVMix requires Python >= 2.7 + </readme> + </package> + + <package name="cython" version="0.19.1"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://cython.org/release/Cython-0.19.1.tar.gz</action> + <action type="make_directory">$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> + </readme> + </package> + + + +</tool_dependency>