Install

SemiBin can run on Python 3.10-3.14.

Install with pixi

The current recommended way to install SemiBin is to use pixi. Pixi will use the packages from conda-forge and bioconda to install SemiBin and its dependencies.

CPU-only mode

Create a pixi.toml file with the following content.

[workspace]
authors = ["Luis Pedro Coelho <luis@luispedro.org>"]
channels = ["conda-forge", "bioconda"]
name = "semibin_install"
platforms = ["linux-64", "osx-64"]
version = "0.1.0"

[tasks]

[dependencies]
semibin = ">=2.3.0,<3"

Then, run pixi install in the same directory as the pixi.toml file to download and install SemiBin2.

With GPU support

If you want to use SemiBin with GPU, you need to install Pytorch with GPU support as well. Starting with the example above, you need to add pytorch-gpu to the dependencies section and cuda to the system-requirements section.

[workspace]
authors = ["Luis Pedro Coelho <luis@luispedro.org>"]
channels = ["conda-forge", "bioconda"]
name = "semibin_install"
platforms = ["linux-64"]
version = "0.1.0"

[tasks]

[dependencies]
semibin = ">=2.3.0,<3"
pytorch-gpu = "*"

[system-requirements]
cuda = "12.0"

Install with conda

Pixi is now the recommended way to install SemiBin. However, if you prefer to use conda, you can install SemiBin with it

Simple Mode

conda create -n SemiBin
conda activate SemiBin
conda install -c conda-forge -c bioconda semibin

With GPU support

To get GPU support, you need to install Pytorch with GPU support as well, following the instructions on the Pytorch website. As of March 2025, it appears that you need to mix conda and pip and the following commands should work:

conda create -n SemiBin python pip
conda activate SemiBin
pip install torch torchvision torchaudio
conda install -c conda-forge -c bioconda semibin

This will install SemiBin and all its dependencies. Pixi is—however—the recommended way to install SemiBin with GPU support.

Install from source

You will need the following dependencies: - Bedtools, Hmmer, Samtools

Optional dependencies: - Prodigal (only needed if using --orf-finder prodigal; the default fast-naive ORF finder does not require it)

You can obtain the required dependencies from conda with the following commands

conda install -c bioconda bedtools hmmer samtools

Then, installing should be a simple matter of running:

pip install .

Alternative ways of running SemiBin

If you use one of these pipelines, we ask that you cite both the pipeline author and the SemiBin manuscript (as well as any other pipeline-embedded tools which contribute to your results).