Building Bio++ and Egglib From Source

It took a little finagling to build the Python module egglib for population genetic analyses. Here’s how I did it.

Platform on which this was tested:

  • OS X 10.7
  • Apple Xcode command line tools
  • Many tools install via Homebrew

Pre-requisites for Bio++

Install the following via brew:

  • cmake – brew install cmake
  • doxygen – brew install doxygen

Building and installing Bio++

Create a temporary directory to build the libraries
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mkdir -p ~/tmp/bpp
Download and unzip the libraires

We just need three of the Bio++ libraries:

  1. bpp-core
  2. bpp-seq
  3. bpp-popgen

Use curl from the command line to download the libraries:

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cd ~/tmp/bpp
curl -O http://biopp.univ-montp2.fr/repos/sources/bpp-core-2.0.3.tar.gz
curl -O http://biopp.univ-montp2.fr/repos/sources/bpp-seq-2.0.3.tar.gz
curl -O http://biopp.univ-montp2.fr/repos/sources/bpp-popgen-2.0.3.tar.gz

And then unzip each library:

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tar xvzf bpp-core-2.0.3.tar.gz
... etc ...
Building individual Bio++ libraries

Build the libraries in the following order:

  1. bpp-core
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cd ~/tmp/bpp/bpp-core-2.0.3
cmake -DCMAKE_INSTALL_PREFIX=/usr/local
make             # warnings are OK, errors are not
make install     # if you didn't get any errors during make
  1. bpp-seq
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cd ~/tmp/bpp/bpp-seq-2.0.3
cmake -DCMAKE_INSTALL_PREFIX=/usr/local
make            
make install
  1. bpp-popgen
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cd ~/tmp/bpp/bpp-popgen-2.0.3
cmake -DCMAKE_INSTALL_PREFIX=/usr/local
make             
make install

Pre-requisites for egglib

These aren’t required but we might as well install them.

First, let’s “tap” the Homebrew science packages:

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brew tap homebrew/science

Then install all the following via brew:

  • gsl – brew install gsl
  • clustalw – brew install clustal-w
  • muscle – brew install muscle
  • paml – brew install paml
  • phyml – brew install phyml
  • primer3 – brew install primer3
  • phylip – brew install phylip

Building and installing egglib

Download the following source packages from the egglib sourceforge site:

  • egglib-cpp-2.1.5.tar.gz
  • egglib-py-2.1.5.tar.gz

Move these to a temporary directory (e.g. ~/tmp/egglib) and unzip them (tar xvzf ....).

Build the egglib c++ library
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cd egglib-cpp-2.1.5
./configure
make
make install  # assuming make return with no errors
Build the egglib Python library

When I tried to build the egglib Python library, setup.py wasn’t finding the appropriate version of gcc for some reason. Here’s how I fixed that (note the addition of the CC environment variable before the setup.py call):

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cd egglib-py-2.1.5
CC=/usr/bin/gcc python setup.py build
CC=/usr/bin/gcc python setup.py install  # assuming previous step was error free

Test your installation of egglib

Confirm that egglib import’s correctly:

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$ python
Python 2.7.3 (v2.7.3:70274d53c1dd, Apr  9 2012, 20:52:43) 
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import egglib
>>> quit()