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 Colab.

Note for macOS users

In general, it is recommended to use Homebrew to install MiGA if possible. The MiGA installation in macOS using conda is known to be fragile and extremely time-consuming (it could take upwards of 20 minutes just solving the environment).

Packages

Now, install all the required packages using conda:

# Install prerequisites
curl -Lso miga.yml \
  "https://raw.githubusercontent.com/bio-miga/miga/main/conda.yml"
conda env create -f miga.yml
rm miga.yml

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

# Activate the environment
. ~/.miga_modules

# Fix conda-forge Ruby issue (see https://github.com/bio-miga/miga/issues/168)
mkdir -p "$GEM_HOME/bin"
ln -s "$CONDA_PREFIX/bin/ruby" "$GEM_HOME/bin/ruby"

MyTaxa utils

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