I didn't find it difficult to install or compile the egglib module on Linux, when I first come to use egglib in python. However, things changed my mind when I was trying to use the internal function Align.polymorphismBPP(), which is a function that depends on the Bio++ library supoort. Somehow, I didn't install the C++ module correctly in the beginning, thus now I need to pay the price.

Before we get into the installation, we need to make sure the pre-requisites by egglib and my local platform configuration.

This tutorial was test on my platform:

  • Ubuntu Linux 14.04LTS
  • Bio-Linux installed
  • Python 2.7.6
  • GCC 4.8.2

Pre-requisites:

  • cmake: sudo apt-get install cmake
  • doxygen: sudo apt-get install doxygen
  • Bio++'s install will be elaborated below

Install dependencies

For egglib-cpp module, you will only need to the three libraries from Bio++: bpp-core, bpp-seq, and bpp-popgen. Keep this mind. I need to mention here, I downloaded everything in the download directory on my server. I am running all the code on an admin account, I ran everything using sudo to get root privilege.

1.Update and upgrade system apps

    sudo apt-get upgrade
    sudo apt-get update

2.Download installation files from Bio++

    mkdir ~/download/bpp
    cd ~/download/bpp
    wget http://biopp.univ-montp2.fr/repos/sources/bpp-core-2.2.0.tar.gz
    wget http://biopp.univ-montp2.fr/repos/sources/bpp-seq-2.2.0.tar.gz
    wget http://biopp.univ-montp2.fr/repos/sources/bpp-popgen-2.2.0.tar.gz

3.Unzip tar files:

    tar xzvf bpp-core-2.2.0.tar.gz  
    tar xzvf bpp-seq-2.2.0.tar.gz  
    tar xzvf bpp-popgen-2.2.0.tar.gz  

4.Compile each module. Make sure you don't have any errors when you try to run the make command

    cd ~/download/bpp/bpp-core-2.2.0
    cmake -DCMAKE_INSTALL_PREFIX=/usr/local
    make # make sure no errors, but warnings should be fine
    make install

    cd ../bpp-seq-2.2.0
    cmake -DCMAKE_INSTALL_PREFIX=/usr/local
    make
    make install

    cd ../bpp-pop-2.2.0
    cmake -DCMAKE_INSTALL_PREFIX=/usr/local
    make
    make install

5.Install linux dependencies for egglib-py. If you already installed the Bio-linux, most of the packages below should be already installed in your system. Just in case, I listed all the dependencies, install them as needed.

  • gsl - GNU Scientific Library: sudo apt-get install libgsl0ldbl
  • clustalw
  • muscle
  • paml
  • phyml
  • primer3
  • phylip

Install egglib

Obtain most recent version of egglib from sourceforge-egglib. You will need download two files for this tutorial:

  • egglib-cpp-2.x.xx.tar.gz
  • egglib-py-2.x.xx.tar.gz

Compile the cpp package:

tar xvzf egglib-cpp-2.1.1.tar.gz
tar xvzf egglib-py-2.1.1.tar.gz
cd egglib-cpp-2.1.11
./configure
make
make install

cd ../egglib-py-2.1.11
sudo python setup.py build
sudo python setup.py install

Test egglib installation

confirm your egglib was installed correctly

Python 2.7.6 (default, Jun 22 2015, 17:58:13)
[GCC 4.8.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import egglib
>>> quit()

References

This tutorial was built based on the resources available online:

[1]. Building Bio++ and Egglib From Source

[2]. tips on installing EggLib on linux