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 Colab.

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/HEAD/install.sh)"

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 3.3.0
rbenv global 3.3.0

Packages

Now that you have Homebrew, execute:

brew tap brewsci/bio
# In Linux, replace 'temurin' with 'openjdk'
brew install \
    r sqlite3 python numpy pigz temurin \
    blast hmmer bedtools prodigal gmp spades mcl krona \
    barrnap diamond fastani faqcs brewsci/bio/falco seqtk fastp trnascan

Additionally, recent changes in pip might break some installations, and as such we recommend pre-installing python packages in a brew environment:

pip install --break-system-packages numpy pyhmmer pyrodigal

We also recommend installing the sqlite3 gem beforehand using the brew libraries, to avoid headaches down the road (but this is optional):

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

MyTaxa utils

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