annotate tool_dependencies.xml @ 1:58279878f849 draft

Uploaded updated xml

<?xml version="1.0"?>
<tool_dependency>
    <package name="readline" version="6.2">
        <repository changeset_revision="ff20613e6fee" name="package_readline_6_2" owner="boris" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="ape" version="3.0-8">
        <repository changeset_revision="423395d792df" name="package_ape_3_0" owner="boris" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="R" version="2.15.0">
        <repository changeset_revision="eca882dd6393" name="package_r_2_15_0" owner="boris" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="rpy2" version="2.2.6">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://pypi.python.org/packages/source/r/rpy2/rpy2-2.2.6.tar.gz</action>
                <action type="set_environment_for_install">
                    <repository changeset_revision="ff20613e6fee" name="package_readline_6_2" owner="boris" toolshed="http://toolshed.g2.bx.psu.edu">
                        <package name="readline" version="6.2" />
                    </repository>
                    <repository changeset_revision="423395d792df" name="package_ape_3_0" owner="boris" toolshed="http://toolshed.g2.bx.psu.edu">
                        <package name="ape" version="3.0-8" />
                    </repository>
                    <repository changeset_revision="eca882dd6393" name="package_r_2_15_0" owner="boris" toolshed="http://toolshed.g2.bx.psu.edu">
                        <package name="R" version="2.15.0" />
                    </repository>
                </action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="shell_command">
                    export R_HOME=$R_HOME &amp;&amp; \
                    export R_LIBS=$R_LIBS &amp;&amp; \
                    export PATH=$PATH &amp;&amp; \
                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; \
                    export CFLAGS="-I$READLINE_INCLUDES" &amp;&amp; \
                    export LDFLAGS="-L$READLINE_LIBS" &amp;&amp; \
                    python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin
                </action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="R_HOME">$ENV[R_HOME]</environment_variable>
                    <environment_variable action="prepend_to" name="R_LIBS">$ENV[R_LIBS]</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH]</environment_variable>
                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>In order to upgrade one will have to first remove older installed rpy2 packages then and only then install the recent version of rpy2 wished.
                Python version 2.5 or greater, as well as R-2.8.0 or greater are required.
                When compiling R from source, do not forget to specify –enable-R-shlib at the ./configure step.
                gcc-4.4 is used for compiling the C parts on Linux.
                If installing from a linux distribution, the Python-dev package will obviously be required to compile rpy2
                On OS X, the XCode tools will be required in order to compile rpy2.</readme>
    </package>
</tool_dependency>