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
date Wed, 16 Dec 2015 07:19:14 -0500
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1:6f8b786e347b 2:c722591ee0aa
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:$INSTALL_DIR/lib/python &amp;&amp;
37 export PATH=$PATH:$PATH_NUMPY &amp;&amp;
38 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp;
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>