Using Conda

You can use conda to install most of the Software required by MiGA. If you don't have Conda, you can follow the Installation instructions.

Live notebook

If you prefer to see code in action, the full installation process with conda is available as a Notebook in Google Collab.

Note for MacOS users

The bioconda fastani recipe currently depends on packages that force downgrading other important packages (including R). This can cause some issues, and we're currently recommending the use of Homebrew whenever possible. If this is not an option for you, a good alternative might be to install FastANI from source instead of using conda. Finally, you could use the instructions below, if the risk of employing old libraries outweights the burden of installation.

Essentials

Now that you have Conda, activate it. If you want to create a separate clean environment (optional) you can simply execute:

conda create -y -n miga python=3.7
conda activate miga

It's strongly recommended to activate conda in the ~/.miga_modules:

# Tell MiGA to activate the proper conda environment:
echo 'eval "$(conda shell.bash hook)" && conda activate miga' > ~/.miga_modules

Next, install the requirements:

conda install -y -c conda-forge r-base r
conda install -y --strict-channel-priority -c conda-forge ruby
conda install -y sqlite openjdk
conda install -y -c conda-forge -c bioconda -c faircloth-lab \
  scythe blast hmmer bedtools prodigal idba mcl barrnap \
  fastqc diamond krona fastani

SolexaQA

There is a version of SolexaQA in conda, but the recipe forced downgrading R and is only available for Linux. Therefore, a safer option is to obtain the precompiled binaries directly from the developers here.

Unzip that file, and locate the appropriate binary in a folder listed in your $PATH.

R packages

The full list of R packages is automatically installed by MiGA. However, we will install one package here to make sure everything is properly initialized.

Rscript -e "install.packages('ape', repos = 'http://cran.rstudio.com/')"

MyTaxa utils

If you want to activate the MyTaxa and MyTaxa Scan steps, follow the instructions to install the MyTaxa Utils.