Mercurial > repos > iuc > package_pybedtools_0_6_6
view tool_dependencies.xml @ 0:cc2ed79fc537 draft
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author | iuc |
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date | Wed, 06 Aug 2014 17:52:14 -0400 |
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children | 9084345ffde3 |
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<?xml version="1.0"?> <tool_dependency> <package name="tabix" version="0.2.6"> <repository changeset_revision="c1743e071a28" name="package_tabix_0_2_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="samtools" version="0.1.19"> <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="bedtools" version="2.19.1"> <repository changeset_revision="3ad963111153" name="package_bedtools_2_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="cython" version="0.20.1"> <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="pybedtools" version="0.6.6"> <install version="1.0"> <actions> <!-- first action is always downloading --> <action type="download_by_url">https://github.com/daler/pybedtools/archive/v0.6.6.tar.gz</action> <!-- populate the environment variables from the dependend repos --> <action type="set_environment_for_install"> <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> <package name="cython" version="0.20.1" /> </repository> </action> <action type="make_directory">$INSTALL_DIR/lib/python</action> <action type="shell_command"> export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin </action> <action type="set_environment"> <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> <environment_variable action="set_to" name="PYTHONPATH_PYBEDTOOLS">$INSTALL_DIR/lib/python</environment_variable> <environment_variable action="set_to" name="PATH_PYBEDTOOLS">$INSTALL_DIR/bin</environment_variable> <environment_variable action="set_to" name="PYBEDTOOLS_ROOT_DIR">$INSTALL_DIR</environment_variable> </action> </actions> </install> <readme>Compiling pybedtools requires cython and the gcc compiler. https://github.com/daler/pybedtools </readme> </package> </tool_dependency>