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
sudo apt-get install cmake
sudo apt-get install doxygen
- Bio++'s install will be elaborated below
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
Obtain most recent version of egglib from sourceforge-egglib. You will need download two files for this tutorial:
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()
This tutorial was built based on the resources available online: