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view tool_dependencies.xml @ 1:14e18dc9ed13

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Build htseq package from source
author Lance Parsons <lparsons@princeton.edu>
date Tue, 04 Sep 2012 14:00:14 -0400
parents 3fdeebd7e710
children 265ca0f35789
line wrap: on
line source

<?xml version="1.0"?>
<tool_dependency>
    <package name="htseq" version="0.5.3p9">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.3p9.tar.gz</action>
                <action type="shell_command">mkdir -p $INSTALL_DIR/lib/python</action>
                <action type="set_environment">
                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
                </action>
                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py build</action>
                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package.
        </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>