Installing RNA velocity on macOS

Package repo: https://github.com/velocyto-team/velocyto.R

At first install necessary library dependencies.

brew install gcc libomp boost

Update your ~/.R/Makevars. It should look similar to the one below.

VER=-9
CC=gcc$(VER)
CXX=g++$(VER)
CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
FLIBS=-L/usr/local/Cellar/gcc/9.2.0/lib/gcc/9/

# This is for open mp
SHLIB_OPENMP_CFLAGS=-Xpreprocessor -fopenmp
SHLIB_OPENMP_CXXFLAGS=-Xpreprocessor -fopenmp

Additional required R packages.

BiocManager::install(c("pcaMethods", "igraph", "h5"))
install.packages("devtools")
devtools::install_github("velocyto-team/velocyto.R")