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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scipy_0_12_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
author iuc
date Tue, 19 May 2015 15:02:23 -0400
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<?xml version="1.0"?>
<tool_dependency>
        <package name="lapack" version="3.4.2">
            <repository changeset_revision="98a7d116c15f" name="package_lapack_3_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
        </package>
        <package name="atlas" version="3.10.1">
            <repository changeset_revision="37ff27ea37ed" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
        </package>
        <package name="numpy" version="1.7.1">
            <repository changeset_revision="c7ae57300a77" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
        </package>
        <package name="scipy" version="0.12.0">
            <install version="1.0">
                <actions>
                    <action type="download_by_url">http://downloads.sourceforge.net/project/scipy/scipy/0.12.0/scipy-0.12.0.tar.gz</action>
                    <action type="set_environment_for_install">
                        <repository changeset_revision="37ff27ea37ed" name="package_atlas_3_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="atlas" version="3.10.1" />
                        </repository>
                        <repository changeset_revision="98a7d116c15f" name="package_lapack_3_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="lapack" version="3.4.2" />
                        </repository>
                        <repository changeset_revision="c7ae57300a77" name="package_numpy_1_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="numpy" version="1.7.1" />
                        </repository>
                    </action>
                    <action type="make_directory">$INSTALL_DIR/lib/python</action>
                    <action language="cheetah" type="template_command">
                    export PYTHONPATH=\$PYTHONPATH:$env.INSTALL_DIR/lib/python &amp;&amp;

                    #if env.get('ATLAS_LIB_DIR', False):
                        export ATLAS=$env.ATLAS_LIB_DIR/libatlas.a &amp;&amp;
                    #end if
                    #if env.get('LAPACK_LIB_DIR', False):
                        export BLAS=$env.LAPACK_LIB_DIR/libblas.a &amp;&amp;
                        export LAPACK=$env.LAPACK_LIB_DIR/liblapack.a &amp;&amp;
                    #end if

                    export PATH=\$PATH:$env.PATH_NUMPY &amp;&amp;
                    export PYTHONPATH=\$PYTHONPATH:$env.PYTHONPATH_NUMPY &amp;&amp;
                    python setup.py install --install-lib $env.INSTALL_DIR/lib/python --install-scripts $env.INSTALL_DIR/bin
                    </action>
                    <action type="set_environment">
                        <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                        <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
                        <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
                        <environment_variable action="set_to" name="PYTHONPATH_SCIPY">$INSTALL_DIR/lib/python</environment_variable>
                        <environment_variable action="set_to" name="PATH_SCIPY">$INSTALL_DIR/bin</environment_variable>
                        </action>
                </actions>
            </install>
            <readme>Compiling scipy requires a C and Fortran compiler (typically gcc and gfortran). The PYTHONPATH for scipy can be accessed through PYTHONPATH_SCIPY and the binaries with PATH_SCIPY.</readme>
        </package>
</tool_dependency>