Mercurial > repos > nml > package_python_3_4_hivtrace_0_1_4
view tool_dependencies.xml @ 1:af0cf1f508fa draft
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 |
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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 $INSTALL_DIR/bin/python3 && export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && export PATH=$PATH:$PATH_NUMPY && export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY && $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>