annotate tool_dependencies.xml @ 1:1ca9f5fd8b65 draft default tip

planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_bioext_0_17_3 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa-dirty

<?xml version="1.0"?>
<tool_dependency>
        <package name="python" version="3.4">
          <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
        </package>
        <package name="pysam" version="0.8.3">
            <repository changeset_revision="085a17b297b1" name="package_python_3_4_pysam_0_8_3" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
        </package>
        <package name="numpy" version="1.10.1">
          <repository changeset_revision="f182da2b1d78" name="package_python_3_4_numpy_1_10_1" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
        </package>
        <package name="scipy" version="0.16">
          <repository changeset_revision="aaeb6262be47" name="package_python_3_4_scipy_0_16" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
        </package>
        <package name="biopython" version="1.66">
          <repository changeset_revision="cb43753d0467" name="package_python_3_4_biopython_1_66" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
        </package>
        <package name="six" version="1.10.0">
          <repository changeset_revision="93036b19115a" name="package_python_3_4_six_1_10_0" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
        </package>
        <package name="bioext" version="0.17.3">
            <install version="1.0">
                <actions>
                    <action type="download_by_url">https://github.com/veg/BioExt/archive/0.17.3.tar.gz</action>
                    <action type="set_environment_for_install">
                        <repository changeset_revision="085a17b297b1" name="package_python_3_4_pysam_0_8_3" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="pysam" version="0.8.3" />
                        </repository>
                        <repository changeset_revision="f182da2b1d78" name="package_python_3_4_numpy_1_10_1" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="numpy" version="1.10.1" />
                        </repository>
                        <repository changeset_revision="aaeb6262be47" name="package_python_3_4_scipy_0_16" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="scipy" version="0.16" />
                        </repository>
                        <repository changeset_revision="cb43753d0467" name="package_python_3_4_biopython_1_66" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="biopython" version="1.66" />
                        </repository>
                        <repository changeset_revision="93036b19115a" name="package_python_3_4_six_1_10_0" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="six" version="1.10.0" />
                        </repository>
                        <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="python" version="3.4" />
                        </repository>
                    </action>
                    <action type="make_directory">$INSTALL_DIR/lib/python</action>
                    <action type="shell_command">
                      export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
                      export PATH=$PATH:$PATH_NUMPY &amp;&amp;
                      export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp;
                      python3 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</environment_variable>
                      <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                      <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_PYSAM]</environment_variable>
                      <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
                      <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_SCIPY]</environment_variable>
                      <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_BIOPYTHON]</environment_variable>
                      <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_SIX]</environment_variable>
                      <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
                      <environment_variable action="prepend_to" name="PATH">$ENV[PATH_SCIPY]</environment_variable>
                      <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                      <environment_variable action="set_to" name="PYTHONPATH_BIOEXT">$INSTALL_DIR/lib/python</environment_variable>
                      <environment_variable action="set_to" name="PATH_BIOEXT">$INSTALL_DIR/bin</environment_variable>
                    </action>
                </actions>
            </install>
            <readme>A few handy bioinformatics tools not already within BioPython</readme>
        </package>
</tool_dependency>