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Bio::Phylo::Beagle - wrapper around the Beagle library This is perl wrapper code that allows one to use Bio::Phylo's data handling capabilities to interface with the Beagle library for likelihood calculations: * Beagle - http://dx.doi.org/10.1093/sysbio/syr100 * Bio::Phylo - http://dx.doi.org/10.1186/1471-2105-12-63 It is based on the SWIG bindings that were orginally developed for python by Simon Frost: http://code.google.com/p/beagle-lib/source/browse/trunk/examples/swig_python/README I developed this on a MacBook Pro with OS X snow leopard. I used the svn revision 1082 of Beagle to build against. I found that I needed to update my SWIG to version 2.0.4, with pcre (both from source). On operating systems that support pkg-config and backticks you should be able to build and install this library. To ensure that everything is OK you should first check to see that pkg-config returns the right values. Try this: pkg-config --cflags hmsbeagle-1 This should return something like the following (exact path may differ depending on your BEAGLE installation): -I/usr/local/include/libhmsbeagle-1 If that is indeed the case, you should be able to build this library using the following commands: perl Makefile.PL make make test (sudo make install) <-- don't do this while these wrappers are experimental The unit test script t/test_simple.t does the same computation as the python test.py script in the Beagle-lib source tree, demonstrating most of the current functionality.