If you prefer to see code in action, the full installation process with homebrew is available as a Notebook in Google Colab.
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 "$(curl -fsSL \https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
It's possible you already have a recent version of ruby (2.3+). To check which version you have, simply run:
ruby -v. If your version of Ruby is older than 2.3, you can install a recent version using:
brew install libyaml rbenvrbenv install 3.0.1rbenv global 3.0.1
Now that you have Homebrew, execute:
brew tap brewsci/biobrew install \r sqlite3 python adoptopenjdk \blast hmmer bedtools prodigal gmp idba mcl krona \barrnap diamond fastani faqcs falco seqtk fastp
We also recommend installing the
sqlite3 gem beforehand using the brew libraries, to avoid headaches down the road (but this is optional):
gem install sqlite3 -- --with-sqlite3-dir="$(brew --prefix sqlite3)"