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fboehm/GEMMA-install-from-source.md

Last active January 11, 2018 04:25
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GEMMA-install-from-source.md

I want to install from source the GEMMA package for mvlmm in genetics studies.

I've cloned the repository. The file GEMMA/Makefile.macosx needs edits.

GEMMA/INSTALL.md lists the dependencies. Since I'm using a mac, I'll try to use homebrew to install these.

GEMMA dependencies

GEMMA runs on Linux and MAC OSX and the runtime has the following dependencies:

  • C++ tool chain >= 4.9
  • GNU Science library (GSL) 1.x (note that 2.x is not yet supported)
  • blas/openblas
  • lapack
  • Eigen3 library
  • zlib

Installing dependencies

I open a terminal and type:

brew install openblas

The installation of openblas requires four dependencies, so homebrew automatically downloaded and installed them. It took some time.

brew install zlib

I then typed

brew install eigen3
brew install lapack

I got an error that eigen3 was already installed, and I was given code that I could use to upgrade to the current version on homebrew. I did that. Analogously, lapack was installed, so I merely needed to upgrade, which itself was optional.

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