Install

The recommended method of installation is through bioconda, using pixi:

pixi global install -c conda-forge -c bioconda macrel

You can also install it with conda (or mamba):

conda install -c bioconda macrel

Run without installing

If you have pixi installed, you can run Macrel directly without installing it first:

pixi exec -c conda-forge -c bioconda macrel

This downloads Macrel (and its dependencies) into a temporary environment and runs it, which is convenient for one-off usage.

Install from source

If you want to use an unreleased version from Github, or tweak the code, we still recommend conda to manage the dependencies. You can install from source by running:

git clone https://github.com/BigDataBiology/Macrel
cd macrel

conda create -n macrel_env
conda activate macrel_env
conda install -y -c conda-forge -c bioconda \
          ngless \
          pyrodigal \
          megahit \
          paladin \
          pandas \
          requests \
          onnxruntime \
          atomicwrites

pip install .

The -c conda-forge -c bioconda channels are required: ngless, megahit, paladin, and pyrodigal are distributed on bioconda and will generally not resolve from the default channels.

Thereafter, to use macrel, activate this environment.

Optional: local AMPSphere querying

Querying the AMPSphere database locally (macrel query-ampsphere --local) with the mmseqs or hmmer modes requires MMSeqs2 and/or HMMER to be installed:

conda install -c bioconda mmseqs2 hmmer

License

Macrel is licensed under the MIT license (see LICENSE file).