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
  • Prerequisites
  • Getting MiGA
  • Getting MiGA source
  • Initializing MiGA
  • Pre-loading Software
  1. Part II: Getting started

Installation

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Last updated 4 years ago

Prerequisites

If you simply want to access projects previously processed, you can skip this step. To install the prerequisites follow .

Getting MiGA

To install MiGA itself, you'll just need:

gem install miga-base

If necessary, you can use sudo gem install miga-base or gem install --user miga-base instead.

Getting MiGA source

If you want to get MiGA working from source instead of using the gem, you can use:

# Get the source. Make sure you use --recursive, to clone submodules:
git clone --recursive https://github.com/bio-miga/miga.git
cd miga

# You can use bundle to make sure you have the required gems,
# or simply install them manually:
bundle

# And finally make MiGA available in the PATH.
# This is not mandatory but it saves time and effort:
echo "export PATH=\"$(pwd)/bin:\$PATH\"" >> ~/.bashrc
source ~/.bashrc

Initializing MiGA

To initialize MiGA for data processing, simply execute and follow the instructions:

miga init

For additional initialization parameters, use miga init -h.

Pre-loading Software

If some of the prerequisites are not already available in your $PATH, you'll have to first tell MiGA how to find them. For that, create (or modify) a bash configuration file at ~/.miga_modules loading any necessary packages. For example, if you're in a cluster architecture using modules, this is where you should load them. Note that some contents may already be present in this file from previous steps. Do not remove or modify those lines if you're not sure what they do. Here's an example of a configuration file for a single computer:

#!/bin/bash
# File: ~/.miga_modules

# Enable software installed in this user
export PATH="$HOME/apps/bin:$PATH"

# Enable MyTaxa
export PATH="$HOME/apps/MyTaxa:$PATH"

Here is an example of a configuration file for a cluster:

#!/bin/bash
# File: ~/.miga_modules

shopt -s expand_aliases
module purge
module load gcc/4.9.0
module load ruby/2.1.5
module load R/3.3.2
module load prodigal/2.6.1
module load bedtools/2.21.0
module load scythe/0.993
module load fastqc/0.11.2
module load idba/1.1.1_kMSS
module load hmmer/3.1b1

# Enable MyTaxa
export PATH="$HOME/shared3/apps/MyTaxa:$PATH"

# Workaround for broken FastQC in the cluster
alias fastqc="perl $(which --skip-alias --skip-functions fastqc)"

# Workaround for broken KronaTools in the cluster
alias ktImportText="perl -I$HOME/shared3/apps/KronaTools-2.5/lib/ \
  $HOME/shared3/bin/ktImportText"

Once you complete this file, rerun:

miga init
system requirements