For Linux, we need to make sure you have development version of OpenSSL installed, so e.g. for Ubuntu run from terminal:

sudo apt-get -y install libssl-dev libcurl4-openssl-dev

Then to install the latest version of R, we need to add the repository, authentication key and install it:

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo add-apt-repository 'deb [arch=amd64,i386] https://cran.rstudio.com/bin/linux/ubuntu xenial/'
sudo apt-get update
sudo apt-get -y install r-base

In R, install devtools package, then use install_github to install the package from source:

install.packages('devtools')
devtools::install_github('benjjneb/dada2')
# Select 1 when prompted to install biocLite
devtools::install_github('taolonglab/himap')

This may take up to about 10 minutes to install on a fresh R installation.

First, make sure you have the latest Xcode and latest R (> 3.4) installed. Then, install Xcode command line tools. To do this, open a macOS Terminal, then type

xcode-select --install

Then open either R console or RStudio and run this:

# Install devtools first
options('install.packages.compile.from.source'='never')
install.packages('devtools')

# DADA2 pre-requisites
source('http://bioconductor.org/biocLite.R')
biocLite('GenomeInfoDbData', suppressUpdates=T)

# DADA2
devtools::install_github('benjjneb/dada2')

# Finally install HiMAP
devtools::install_github('taolonglab/himap')

• Human gut microbiome data tutorial (main tutorial with all explanations)
• mock community tutorial

By default, multithreading is enabled and supported only on Linux and macOS, through R package parallel.