view tool_dependencies.xml @ 10:d7dedd95ac6f draft

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<?xml version="1.0"?>
<tool_dependency>
    <package name="numpy" version="1.9">
        <repository changeset_revision="507f3ab4e38d" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    
    <package name="cython" version="0.20.1">
        <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    
    <package name="crossmap" version="0.1.8">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/crossmap/files/CrossMap-0.1.8.tar.gz</action>
                
                <action type="setup_python_environment">
                    <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="cython" version="0.20.1" />
                    </repository>
                    <repository changeset_revision="507f3ab4e38d" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="numpy" version="1.9" />
                    </repository>
                </action>
                
                <!-- CrossMap doesn't pick up the correct Cython path.
                Therefore install it with a manual shell_command instead
                of <package></package> inside the pyton_env. -->
                <action type="shell_command">
                    export PYTHONPATH="$CYTHON_PATH/lib/python/Cython-0.20.1-py2.7-linux-x86_64.egg:$PYTHONPATH" &amp;&amp;
                    
                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
                    python setup.py install --install-dir $INSTALL_DIR --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
                </action>
                
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/site-packages</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/usr/local/bin</environment_variable>
                    
                    <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/usr/local/bin</environment_variable>
                    <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
CrossMap is versatile tool to convert genome coordinates or annotation files between genome
assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
and VCF, reading from remote servers and file compression are supported.

Installation

Prerequisite:
 * gcc
 * python2.7 or newer
 * numpy
 * cython

Download CrossMap program from here:

$ tar zxf CrossMap-VERSION.tar.gz

$ cd CrossMap-VERSION

# install CrossMap to default location. In Linux/Unix, this location is like:
# /home/user/lib/python2.7/site-packages/
$ python setup.py install

# or you can install CrossMap to a specified location:
$ python setup.py install --root=/home/user/CrossMap

# setup PYTHONPATH. Skip this step if CrossMap was installed to default location.
$ export PYTHONPATH=/home/user/CrossMap/usr/local/lib/python2.7/site-packages:$PYTHONPATH.

# Skip this step if CrossMap was installed to default location.
$ export PATH=/home/user/CrossMap/usr/local/bin:$PATH

NOTE:

 * Due to intensive computation, CrossMap is designed to run on Linux/Unix and Mac OS. Some modules may not work properly on Windows.
 * Mac users need to download and install Xcode command line tools.

Documentation: http://crossmap.sourceforge.net/
        </readme>
    </package>
</tool_dependency>