Installation

Important

Since release v0.10.2, CHAMOIS can now run on Windows! This uses the PyHMMER v0.12.0 experimental MinGW-w64 build which supports Windows 10 and later. See the PyHMMER documentation for more information about Windows support.

Local Setup

PyPi

CHAMOIS is hosted on GitHub, but the easiest way to install it is to download the latest release from its PyPi repository. It will install all dependencies, then install CHAMOIS and its required data:

$ pip install --user chamois-tool

Conda

CHAMOIS is also available as a recipe in the bioconda channel. To install, simply use the conda installer:

$ conda install bioconda::chamois

GitHub + pip

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

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

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/CHAMOIS
$ cd CHAMOIS
$ 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.

Containers

Docker

CHAMOIS is also distributed in a Docker container for reproducibility. An image is built for every release. To get the latest image, run:

$ docker pull ghcr.io/zellerlab/chamois

Then, to run the image and analyze files in the local directory, make sure to mount the currend working directory to the /io volume, enable terminal emulation with -t to get a nice output, and run the rest of the command line interface normally:

$ docker run -v $(pwd):/io -t ghcr.io/zellerlab/chamois predict -i tests/data/BGC0000703.4.gbk -o tests/data/BGC0000703.4.hdf5

Singularity / Apptainer

A recipe for Singularity / Apptainer containers is available in the project repository. Clone the repository and then build the image with:

$ git clone https://github.com/zellerlab/CHAMOIS
$ cd CHAMOIS
$ singularity build --fakeroot chamois.sif pkg/singularity/chamois.def

Then run the image and analyze the files in the local directory:

$ singularity run chamois.sif predict -i tests/data/BGC0000703.4.gbk -o tests/data/BGC0000703.4.hdf5