MiGA Manual
AboutCodebaseMiGA Online
Primary version
Primary version
  • Introduction
  • Part I: What is MiGA?
    • How can MiGA help me?
    • Who is using MiGA?
    • Who is behind MiGA?
    • Definitions
  • Part II: Getting started
    • Requirements
      • Using Homebrew
      • Using apt-get
      • Using Conda
      • Installing from source
      • MyTaxa Utils
    • Installation
    • MiGA types
    • Input data
    • Distances
    • Clustering
  • Part III: Interfaces
    • MiGA API
    • MiGA CLI
    • MiGA Web
  • Part IV: Deploying examples
    • RefSeq in MiGA
    • Build a clade collection
    • Launching daemons
    • Setting up MiGA in a cluster
  • Part V: Additional details
    • Advanced configuration
    • MiGA workflow
    • Metadata
    • External Software
  • Part VI: Workflows
    • Quality
    • Dereplicate
    • Classify
    • Preprocess
    • Index
    • Summaries
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On this page
  • Live notebook
  • Installing requirements using Homebrew
  • Essentials
  • A recent Ruby
  • R packages
  • MyTaxa utils
  1. Part II: Getting started
  2. Requirements

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.

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Last updated 4 years ago