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 userexport PATH="$HOME/apps/bin:$PATH"# Enable MyTaxaexport PATH="$HOME/apps/MyTaxa:$PATH"
Here is an example of a configuration file for a cluster:
#!/bin/bash# File: ~/.miga_modulesshopt -s expand_aliasesmodule purgemodule load gcc/4.9.0module load ruby/2.1.5module load R/3.3.2module load prodigal/2.6.1module load bedtools/2.21.0module load scythe/0.993module load fastqc/0.11.2module load idba/1.1.1_kMSSmodule load hmmer/3.1b1# Enable MyTaxaexport PATH="$HOME/shared3/apps/MyTaxa:$PATH"# Workaround for broken FastQC in the clusteralias fastqc="perl $(which --skip-alias --skip-functions fastqc)"# Workaround for broken KronaTools in the clusteralias ktImportText="perl -I$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.
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.
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.gitcd 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\"" >> ~/.bashrcsource ~/.bashrc
To initialize MiGA for data processing, simply execute and follow the instructions:
To see additional initialization parameters, use
miga init -h.