Mercurial > repos > ulfschaefer > package_python_2_7_biopython_1_66
comparison tool_dependencies.xml @ 2:c722591ee0aa draft default tip
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author | ulfschaefer |
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date | Wed, 16 Dec 2015 07:19:14 -0500 |
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1:6f8b786e347b | 2:c722591ee0aa |
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1 <?xml version="1.0"?> | |
2 <tool_dependency> | |
3 <package name="python" version="2.7.10"> | |
4 <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
5 </package> | |
6 <package name="numpy" version="1.9"> | |
7 <repository changeset_revision="794f5cf3bb5d" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
8 </package> | |
9 <package name="biopython" version="1.66"> | |
10 <readme> | |
11 This package is a modified version of the package package_biopython_1_66 | |
12 owned by 'biopython' (copyright Peter Cock) revision 8433ee4531ff. | |
13 Dependencies of this package have been modified to provide Biopython | |
14 for Python 2.7.10. | |
15 | |
16 This Galaxy Tool Shed package installs Biopython from source, having | |
17 first installed NumPy which is a build time depencency. This requires | |
18 and assumes a standard C compiler is already installed, along with | |
19 the Python header files. | |
20 | |
21 Development of this dependency definition is being done here on GitHub: | |
22 https://github.com/biopython/galaxy_packages | |
23 | |
24 The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON. | |
25 </readme> | |
26 <install version="1.0"> | |
27 <actions> | |
28 <action type="download_by_url">https://pypi.python.org/packages/source/b/biopython/biopython-1.66.tar.gz</action> | |
29 <action type="set_environment_for_install"> | |
30 <repository changeset_revision="794f5cf3bb5d" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> | |
31 <package name="numpy" version="1.9" /> | |
32 </repository> | |
33 </action> | |
34 <action type="make_directory">$INSTALL_DIR/lib/python</action> | |
35 <action type="shell_command"> | |
36 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && | |
37 export PATH=$PATH:$PATH_NUMPY && | |
38 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY && | |
39 python setup.py install --install-lib $INSTALL_DIR/lib/python | |
40 </action> | |
41 <action type="set_environment"> | |
42 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> | |
43 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable> | |
44 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable> | |
45 <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable> | |
46 </action> | |
47 </actions> | |
48 </install> | |
49 </package> | |
50 </tool_dependency> |