Installation Guide

There are multiple ways to install alignoth:

Pixi

Alignoth can be easily installed globally using pixi:

pixi global install alignoth

Bioconda

Alignoth is available via Bioconda. With Bioconda set up, installation is as easy as:

conda install alignoth -c conda-forge -c bioconda -c nodefaults

Pay attention to the correct channel ordering for the installation.

Cargo

If the Rust compiler and associated Cargo are installed, alignoth may be installed via:

cargo install alignoth

Docker

Alignoth is also available as a prebuilt container through Biocontainers. This image provides a ready-to-use environment with all dependencies preinstalled, making it convenient for users who prefer containerized workflows or encounter issues with native installations.

To pull and run the image directly from Quay.io, use:

docker pull quay.io/biocontainers/alignoth:<version>
docker run --rm quay.io/biocontainers/alignoth:<version> alignoth --help

Replace <version> with the desired release tag (e.g., 0.16.4--h1520f10_0). A list of all available versions can also be found on the Biocontainers page.

Source

Download the source code and within the root directory of source run:

cargo install