Mercurial > repos > nml > package_python_3_4_hivtrace_0_1_4

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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa-dirty
author nml
date Thu, 07 Jul 2016 13:43:14 -0400
parents 38541eaf0d20
children 8ba7ea2370cb
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<?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="cmake" version="3.2.3">
      <repository changeset_revision="1aea698a1c63" name="package_cmake_3_2_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="hyphy-python" version="0.1.3">
      <repository changeset_revision="5c14a49141f0" name="package_python_3_4_hyphy_python_0_1_3" owner="nml" 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="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="bioext" version="0.17.3">
      <repository changeset_revision="1ca9f5fd8b65" name="package_python_3_4_bioext_0_17_3" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="cython" version="0.23.4">
      <repository changeset_revision="52c11d398790" name="package_python_3_4_cython_0_23_4" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="fakemp" version="0.9.1">
      <repository changeset_revision="13da2754601c" name="package_python_3_4_fakemp_0_9_1" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="hppy" version="0.9.6">
      <repository changeset_revision="46decde5b780" name="package_python_3_4_hppy_0_9_6" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="hivclustering" version="1.2.3">
      <repository changeset_revision="eda1cbde6572" name="package_python_3_4_hivclustering_1_2_3" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="tn93" version="1.0.2">
      <repository changeset_revision="e1abbe60f3d4" name="package_tn93_1_0_2" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="hivtrace" version="0.1.4">
        <install version="1.0">
          <actions>
            <action type="download_by_url">https://github.com/veg/hivtrace/archive/0.1.4.tar.gz</action>
            <action type="set_environment_for_install">
                <repository changeset_revision="5c14a49141f0" name="package_python_3_4_hyphy_python_0_1_3" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
                    <package name="hyphy-python" version="0.1.3" />
                </repository>
                <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="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="1ca9f5fd8b65" name="package_python_3_4_bioext_0_17_3" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
                    <package name="bioext" version="0.17.3" />
                </repository>
                <repository changeset_revision="eda1cbde6572" name="package_python_3_4_hivclustering_1_2_3" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
                    <package name="hivclustering" version="1.2.3" />
                </repository>
                <repository changeset_revision="52c11d398790" name="package_python_3_4_cython_0_23_4" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
                    <package name="cython" version="0.23.4" />
                </repository>
                <repository changeset_revision="13da2754601c" name="package_python_3_4_fakemp_0_9_1" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
                    <package name="fakemp" version="0.9.1" />
                </repository>
                <repository changeset_revision="46decde5b780" name="package_python_3_4_hppy_0_9_6" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
                    <package name="hppy" version="0.9.6" />
                </repository>
                <repository changeset_revision="e1abbe60f3d4" name="package_tn93_1_0_2" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
                    <package name="tn93" version="1.0.2" />
                </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">$INSTALL_DIR/lib/python</action>
            <action type="make_directory">$INSTALL_DIR/bin</action>
            <action type="shell_command">
              ln -s $PATH_PYTHON3/python3 $INSTALL_DIR/bin/python3 &amp;&amp;
              export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
              export PATH=$PATH:$PATH_NUMPY &amp;&amp;
              export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp;
              $INSTALL_DIR/bin/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/lib/python</environment_variable>
              <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
              <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_BIOPYTHON]</environment_variable>
              <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_BIOEXT]</environment_variable>
              <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
              <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_PYSAM]</environment_variable>
              <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_HYPHY_PYTHON]</environment_variable>
              <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_CYTHON]</environment_variable>
              <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_HIVCLUSTERING]</environment_variable>
              <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_FAKEMP]</environment_variable>
              <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_HPPY]</environment_variable>
              <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
              <environment_variable action="prepend_to" name="PATH">$ENV[PATH_PYSAM]</environment_variable>
              <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
              <environment_variable action="prepend_to" name="PATH">$ENV[PATH_HIVCLUSTERING]</environment_variable>
              <environment_variable action="prepend_to" name="PATH">$ENV[PATH_BIOEXT]</environment_variable>
              <environment_variable action="prepend_to" name="PATH">$ENV[PATH_TN93]</environment_variable>
            </action>
          </actions>
        </install>
        <readme>
This installs hivtrace 0.1.4 (and all its dependencies).

See usage instructions here: https://github.com/veg/hivtrace
        </readme>
    </package>
</tool_dependency>