Installing#

Important

IGUA is a Python library but relies on MMseqs2 to handle the different clustering stages. Most installation modes will also ensure the mmseqs binary is installed on your machine or bundle a working MMseqs2 install (if using a container). However, for direct Python installs with pip, you will need to ensure yourself that MMseqs2 is available.

Conda#

IGUA and all of its dependencies are available via Bioconda and can be installed using e.g., conda or pixi:

  1. First, set up Bioconda with Pixi or Conda..

  2. Then, install IGUA using the appropriate method:

    • With conda:

      $ conda install igua

    • With pixi:

      $ pixi add igua

Apptainer, Docker, and Singularity#

IGUA (and all of its dependencies) can be run using e.g., Docker, Apptainer, and Singularity, using images available on quay.io.

For instance, to install IGUA 0.1.0 with AppTainer, use:

$ apptainer pull docker://quay.io/biocontainers/igua:0.1.0--py39h5b94c0b_0

PyPi#

IGUA can be downloaded directly from PyPI, which hosts pre-compiled distributions for Linux, MacOS and Windows. To install IGUA with pip, use:

$ pip install --user igua

Note that you need to have a working install of MMSeqs2 on your system, as MMseqs2 cannot be installed directly from PyPI.

Arch User Repository#

A package recipe for Arch Linux can be found in the Arch User Repository under the name igua. It will always match the latest release from PyPI.

Steps to install on ArchLinux depend on your AUR helper (yaourt, aura, yay, etc.). For aura, you’ll need to run:

$ aura -A igua

GitHub + pip#

If, for any reason, you prefer to download the library from GitHub, you can clone the repository and install the repository by running (with the admin rights):

$ pip install -U git+https://github.com/zellerlab/IGUA

Caution

Keep in mind this will install always try to install the latest commit, which may not even build, so consider using a versioned release instead.

GitHub + build#

If you do not want to use pip, you can still clone the repository and use build and installer manually:

$ git clone https://github.com/zellerlab/IGUA
$ cd IGUA
$ python -m build .
# python -m installer dist/*.whl

Danger

Installing packages without pip is strongly discouraged, as they can only be uninstalled manually, and may damage your system.