Mercurial > repos > biopython > package_biopython_1_62

comparison tool_dependencies.xml @ 0:3e82cbc44886 draft

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Uploaded initial version, based on setup used for Biopython 1.61
author biopython
date Tue, 17 Sep 2013 04:56:33 -0400
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children f06c96348778
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-1:000000000000 0:3e82cbc44886
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="numpy" version="1.7.1">
4 <repository changeset_revision="74c21f9bdc39" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="biopython" version="1.62">
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>
18 <install version="1.0">
19 <actions>
20 <action type="download_by_url">https://pypi.python.org/packages/source/b/biopython/biopython-1.62.tar.gz</action>
21 <action type="set_environment_for_install">
22 <repository changeset_revision="74c21f9bdc39" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
23 <package name="numpy" version="1.7.1" />
24 </repository>
25 </action>
26 <action type="make_directory">$INSTALL_DIR/lib/python</action>
27 <action type="shell_command">
28 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
29 export PATH=$PATH:$PATH_NUMPY &amp;&amp;
30 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp;
31 python setup.py install --install-lib $INSTALL_DIR/lib/python
32 </action>
33 <action type="set_environment">
34 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
35 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
36 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
37 <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
38 </action>
39 </actions>
40 </install>
41 </package>
42 </tool_dependency>