Mercurial > repos > biopython > package_biopython_1_61
comparison tool_dependencies.xml @ 3:2f6c871cfa35 draft
Remove last bit of MatPlotLib
| author | peterjc |
|---|---|
| date | Tue, 17 Sep 2013 04:49:17 -0400 |
| parents | 54e5c64b0460 |
| children | 89f98445faf4 |
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| 2:54e5c64b0460 | 3:2f6c871cfa35 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="numpy" version="1.7.1"> | 3 <package name="numpy" version="1.7.1"> |
| 4 <repository changeset_revision="793c48909d53" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> | 4 <repository changeset_revision="b7ff4a8c58df" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> |
| 5 </package> | 5 </package> |
| 6 <package name="biopython" version="1.61"> | 6 <package name="biopython" version="1.61"> |
| 7 <readme> | |
| 8 This Galaxy Tool Shed package installs Biopython from source, having | |
| 9 first installed NumPy which is a build time depencency. This requires | |
| 10 and assumes a standard C compiler is already installed, along with | |
| 11 the Python header files. | |
| 12 | |
| 13 Development of this dependency definition is being done here on GitHub: | |
| 14 https://github.com/biopython/galaxy_packages | |
| 15 | |
| 16 The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON. | |
| 17 </readme> | |
| 7 <install version="1.0"> | 18 <install version="1.0"> |
| 8 <actions> | 19 <actions> |
| 9 <action type="download_by_url">https://pypi.python.org/packages/source/b/biopython/biopython-1.61.tar.gz</action> | 20 <action type="download_by_url">https://pypi.python.org/packages/source/b/biopython/biopython-1.61.tar.gz</action> |
| 10 <action type="set_environment_for_install"> | 21 <action type="set_environment_for_install"> |
| 11 <repository changeset_revision="793c48909d53" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> | 22 <repository changeset_revision="b7ff4a8c58df" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> |
| 12 <package name="numpy" version="1.7.1" /> | 23 <package name="numpy" version="1.7.1" /> |
| 13 </repository> | 24 </repository> |
| 14 </action> | 25 </action> |
| 15 <action type="make_directory">$INSTALL_DIR/lib/python</action> | 26 <action type="make_directory">$INSTALL_DIR/lib/python</action> |
| 16 <action type="shell_command"> | 27 <action type="shell_command"> |
| 17 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && | 28 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && |
| 18 export PATH=$PATH:$PATH_NUMPY && | 29 export PATH=$PATH:$PATH_NUMPY && |
| 19 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY:$PYTHONPATH_MATPLOTLIB && | 30 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY && |
| 20 python setup.py install --install-lib $INSTALL_DIR/lib/python | 31 python setup.py install --install-lib $INSTALL_DIR/lib/python |
| 21 </action> | 32 </action> |
| 22 <action type="set_environment"> | 33 <action type="set_environment"> |
| 23 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> | 34 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> |
| 24 | |
| 25 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable> | 35 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable> |
| 26 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable> | 36 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable> |
| 27 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable> | |
| 28 | |
| 29 <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable> | 37 <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable> |
| 30 </action> | 38 </action> |
| 31 </actions> | 39 </actions> |
| 32 </install> | 40 </install> |
| 33 <readme>The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON.</readme> | |
| 34 </package> | 41 </package> |
| 35 </tool_dependency> | 42 </tool_dependency> |