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Installation

Prerequisites

If you simply want to access projects previously processed, you can skip this step.

Once you have satisfied all the system requirements, you'll need to make them accessible to MiGA. For that, create a bash configuration file at ~/.miga_modules loading any necessary packages (e.g., if you're in a cluster architecture using modules, this is where you should load them). 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"

If all of the requirements are readily available (e.g., if you already registered them in your ~/.bashrc), this file can be empty or nonexistent.

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, so you also 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 completely necessary,
# 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

To see additional initialization parameters, use miga init -h.