Installation

Note

Supported Python versions are 3.12, 3.13 and 3.14.

Tip

cfoldseeker’s remote mode requires a local copy of UniProt’s ID mapping table. We have prepared a ready-to-use reduced version from the 2026_01 release only containing the KEGG and GenPept rows. We attach it to every GitHib release as uniprot_kegg_genpept.gz.

Conda (recommended)

This is the recommended and most straightforward way to install cfoldseeker. It should work on any Linux or MacOS system. Create a fresh conda environment as well to keep it from meddling with your other tools. It is directly installable from Bioconda

conda create -n cfoldseeker -c bioconda -c conda-forge cfoldseeker

or by using the conda yml environment file in this repo.

conda env create -f env.yml

Then start using it by activating the conda environment.

conda activate cfoldseeker

Docker

cfoldseeker is also available as a Docker image from DockerHub. This is one of the recommended ways to run cfoldseeker on Windows (the other one being running it using Windows’ WSL feature).

docker pull lucodevro/cfoldseeker

There is no entrypoint set up so running cfoldseeker requires prepending your cfoldseeker command with the appropriate Docker commands.

docker run lucodevro/cfoldseeker -v <some-input-file-or-folder>:<path-you-want-it-inside-the-container> cfoldseeker [-<flags>] [arguments]

GitHub

Alternatively, it is possible to install the latest semi-stable development version by cloning this repository and running the following command at the root of your local copy of this repository.

pip install .

PyPi

cfoldseeker is also installable from PyPi using pip, yet we do not recommend using this approach as its core dependency FoldSeek is not available from PyPi, and therefore should be installed beforehand. So either make sure you have installed it separately, or use one of the other installation options.

pip install cfoldseeker

Warning

We do not recommend using this approach as key non-Python dependencies are not available from PyPi (FoldSeek) and therefore should be installed beforehand. Check out cfoldseeker’s dependencies in the Bioconda recipe for more details.