Using Homebrew

Live notebook

If you prefer to see code in action, the full installation process with homebrew is available as a Notebook in Google Collab.

Installing requirements using Homebrew

You can use Homebrew to install most of the software required by MiGA. If you don't have Homebrew, execute (and follow the instructions):

/bin/bash -c "$(curl -fsSL \
  https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"

Next, make sure you have the brewsci/bio tap:

brew tap brewsci/bio

Essentials

Now that you have Homebrew and the science tap, execute:

# General-purpose software
brew install r sqlite3 python adoptopenjdk
# Bioinformatics software
brew install blast hmmer bedtools \
      prodigal idba mcl barrnap fastqc solexaqa \
      diamond fastani
brew install jonchang/biology/scythe
# Pending: Scythe in science (contacting authors)
# See: https://github.com/brewsci/homebrew-bio/issues/23
# See also: https://github.com/vsbuffalo/scythe/pull/20

A recent Ruby

It's possible you already have a recent version of ruby (2.3+). To check which version you have, simply run: ruby -v. If your version of Ruby is older than 2.3, you can install a recent version using:

brew install libyaml rbenv
rbenv install 2.7.1
rbenv global 2.7.1

We also recommend installing the sqlite3 gem beforehand using the brew libraries, to avoid headaches down the road:

gem install sqlite3 -- --with-sqlite3-dir="$(brew --prefix sqlite3)"

R packages

The full list of R packages is automatically installed by MiGA. However, we will install one package here to make sure everything is properly initialized.

Rscript -e "install.packages('ape', repos = 'http://cran.rstudio.com/')"

MyTaxa utils

If you want to activate the MyTaxa and MyTaxa Scan steps, follow the instructions to install the MyTaxa Utils.