Installation

Building from source

If using the Docker image is not possible or preferable, the source code of the current development version can be downloaded using git:

> git clone https://bitbucket.org/kbhoehn/igphyml
> cd igphyml

Requirements

  • GNU autoconf
  • GNU automake
  • (optional) Change-O 0.4.6
  • (optional) Alakazam 0.3.0
  • (optional) OpenMP-enabled C compiler (e.g. gcc or LLVM)
  • (optional) BLAS and LAPACK optimization libraries

Linux

On Linux operating systems, you can usually just run:

./make_phyml_omp

If you have BLAS and LAPACK installed, which provide libraries for faster and more accurate matrix exponentiation operations. In Ubuntu Linux, these are provided in the packages libblas-dev and liblapack-dev. Other distros probably have similar package names. To compile IgPhyML with BLAS and LAPACK support, run:

./make_phyml_blas_omp

If OpenMP is also not available, IgPhyML may be compiled without it, but this will substantially reduce performance on multicore machines:

./make_phyml

Once everything is compiled, add the igphyml/src directory to your PATH variable, and IgPhyML should work. Importantly, some directory files are hardcoded in at compilation, so re-compile IgPhyML if you move the installation directory. Alternatively, you can set the IGPHYML_PATH environment variable to the location of the igphyml/src/motifs folder for the same effect.

Mac OS X

Installation on Mac OS X is trickier, but possible. The primary issue is gaining OpenMP support, and installing some GNU command line tools. The best way is to just install the latest version of llvm available through homebrew, as well as autoconf and automake. To do these you’ll need to install homebrew. If it’s already installed be sure it’s at the latest version (brew update). You may need to install Xcode as well. Next, install autoconf, automake, and llvm:

brew install autoconf
brew install automake
brew install llvm

Specify the llvm version of clang in Makefile.am and src/Makefile.am by adding the line CC=<path to llvm clang> to the beginning of both files. You will also need to add MACOMP=<path to omp.h> and MACLLVM=<path to llvm lib> to src/Makefile.am. For instance, if you’ve install llvm 3.9.1 via homebrew, you will likely need to add the line CC=/usr/local/Cellar/llvm/3.9.1/bin/clang to Makefile.am and the lines:

CC=/usr/local/Cellar/llvm/3.9.1/bin/clang
MACOMP=/usr/local/Cellar/llvm/3.9.1/lib/clang/3.9.1/include/omp.h
MACLLVM=/usr/local/Cellar/llvm/3.9.1/lib

to src/Makefile.am. Your specific path may look different, but you can check locations of these files and folders by looking around in /usr/local/Cellar/llvm/. The directory structure should be similar. Run ./make_blas_phyml_omp, or other versions, as desired, and add the src folder to your PATH variable.

On some versions of OS X it may be necessary to install XCode command line tools using:

xcode-select --install
cd /Library/Developer/CommandLineTools/Packages/
open macOS_SDK_headers_for_macOS_<OS X version>.pkg