Mercurial > repos > mzeidler > virana2

view tool_dependencies.xml @ 57:937aad0e7a96 draft

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author mzeidler
date Sun, 29 Sep 2013 11:30:35 -0400
parents f5b57fd8378a
children a6ce4aa4cb6e
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line source

<tool_dependency>
    <package name="virana_python" version="1.0">
        <install version="1.0">
            <actions>
                <action type="setup_virtualenv"> 
                    http://downloads.sourceforge.net/project/numpy/NumPy/1.6.0/numpy-1.6.0.tar.gz
                    https://github.com/zeidlermicha/virana/raw/master/Virana-1.0.0.tar.gz
                                                 </action>
            </actions>
        </install>
    </package>
    <package name="samtools" version="0.1.19">
        <install>
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>samtools</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>
    </package>
    <package name="bwa" version="0.7.4">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/bio-bwa/files/bwa-0.7.4.tar.bz2 </action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>bwa</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>
    </package>
    
    <package name="STAR" version="2.3.0" >
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://rna-star.googlecode.com/files/STAR_2.3.0e.tgz</action>
                <action type="move_file">
                    <source>STAR</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>
    
    </package>
    <package name="lastz" version="1.02.00" >
        <install version="1.0">
            <actions>
                <action type="download_by_url" target_filename="lastz-distrib-1.02.00.tar.gz">http://www.bx.psu.edu/miller_lab/dist/lastz-1.02.00.tar.gz</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                         <source>src/lastz</source>
                         <destination>$INSTALL_DIR/bin</destination>
                     </action>
                     <action type="move_file">
                         <source>src/lastz_D</source>
                         <destination>$INSTALL_DIR/bin</destination>
                     </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
    </package>
</tool_dependency>