view tool_dependencies.xml @ 21:b64dcea4531a draft

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<?xml version="1.0"?>
<tool_dependency>
    <package name="numpy" version="1.7.1">
       <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="scipy" version="0.12.0">
       <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="R_3_0_1" version="3.0.1">
        <repository changeset_revision="1c0e86a44f73" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="gnu_awk" version="4.1.0">
       <repository changeset_revision="cbe9f1c8c98b" name="package_gnu_awk_4_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <set_environment version="1.0">
        <environment_variable action="set_to" name="MACS2_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>
    <!-- 2.0.10 12162013 -->
    <package name="macs2" version="2.0.10.3">
        <install version="1.0">
            <actions>
                <action type="shell_command">git clone --recursive https://github.com/taoliu/MACS.git</action>
                <!-- Galaxy tries to change automatically to the directory "macs2" (name of the package). 
                But we need to change to MACS. Go one level back and enter MACS -->
                <action type="change_directory">../MACS</action>
                <action type="shell_command">git checkout 7ccb571d2f2dcb5be1d75f323b1d17a59b926deb</action>
                <action type="shell_command">git submodule update --recursive</action>

                <action type="set_environment_for_install">
                    <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                        <package name="numpy" version="1.7.1" />
                    </repository>
                    <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                        <package name="scipy" version="0.12.0" />
                    </repository>
                </action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <!-- exporting the CFLAGS and CPPFLAGS are due to http://stackoverflow.com/questions/22313407/clang-error-unknown-argument-mno-fused-madd-python-package-installation-fa -->
                <action type="shell_command">
                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
                    python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
                </action>
                <action type="set_environment">
                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_SCIPY]</environment_variable>
                    <environment_variable action="set_to" name="PYTHONPATH_MACS2">$INSTALL_DIR/lib/python</environment_variable>
                    </action>
            </actions>
        </install>
        <readme>Macs2 installation instructions. MACS2 can be found at https://github.com/taoliu/MACS</readme>
    </package>
</tool_dependency>