MiGA Manual
AboutCodebaseMiGA Online
main
main
  • 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
Powered by GitBook
On this page
  • Live notebook
  • Installing requirements using Homebrew
  • A recent Ruby
  • Packages
  • MyTaxa utils
  1. Part II: Getting started
  2. Requirements

Using Homebrew

PreviousRequirementsNextUsing apt-get

Last updated 9 months ago

Live notebook

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

Installing requirements using Homebrew

You can use 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 idba 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 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 and steps, follow the instructions to install the .

Notebook in Google Colab
Homebrew
MyTaxa
MyTaxa Scan
MyTaxa Utils