Installation

Prerequisites

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

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 spades/4.0
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