|
0
|
1 <?xml version="1.0"?>
|
|
|
2 <tool_dependency>
|
|
|
3 <package name="python" version="2.7.10">
|
|
|
4 <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
|
|
|
5 </package>
|
|
|
6 <package name="numpy" version="1.9">
|
|
|
7 <repository changeset_revision="fe0870696ca7" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.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="fe0870696ca7" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.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>
|
