If you simply want to access projects previously processed, you can skip this step. To install the prequisites follow system requirements.
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, to 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 mandatory 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:
For additional initialization parameters, use
miga init -h.
If some of the prerequisites are not already available in your
$PATH, you'll have to first tell MiGA how to find them. For that, create (or modify) a
bash configuration file at
~/.miga_modules loading any necessary packages. For example, if you're in a cluster architecture using
modules, this is where you should load them. Note that some contents may already be present in this file from previous steps. Do not remove or modify those lines if you're not sure what they do. Here's an example of a configuration file for a single computer:
#!/bin/bash# File: ~/.miga_modules# Enable software installed in this userexport PATH="$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"
Once you complete this file, rerun: