In KasperSkytte/mmgenome2: Tools for extracting individual genomes from metagenomes

One of the dependencies (Rtsne) that mmgenome2 uses requires the following to be able to compile and install correctly on MAC:

• Open a terminal (cmd+space and type "terminal")
• Install homebrew (a software manager for OSX) as described on their website https://brew.sh/
• run: brew uninstall gcc
• run: brew install gcc --without-multilib
• create a .R folder in your home directory by mkdir ~/.R
• create a Makevars file in the folder by nano ~/.R/Makevars and paste the following, save the file afterwards by ctrl+x followed by "y":

CC=/usr/local/bin/gcc-7
CXX=/usr/local/bin/g++-7
CXX1X=/usr/local/bin/g++-7
CXX11=/usr/local/bin/g++-7
SHLIB_CXXLD=/usr/local/bin/g++-7
FC=/usr/local/bin/gfortran-7
F77=/usr/local/bin/gfortran-7
MAKE=make -j8

SHLIB_OPENMP_CFLAGS=-fopenmp
SHLIB_OPENMP_CXXFLAGS=-fopenmp
SHLIB_OPENMP_FCFLAGS=-fopenmp
SHLIB_OPENMP_FFLAGS=-fopenmp

Now mmgenome2 can be installed normally as described at the mmgenome2 webpage. If you have RStudio open then you must restart the current R-session (ctrl+shift+F10) before installing mmgenome2.

KasperSkytte/mmgenome2 documentation built on Dec. 14, 2021, 12:11 a.m.