Installation

We recommend using Docker or Singularity - built containers are available for each release. Alternatively, you can install from the source code.

Docker

Get a Docker image of the latest release:

docker pull ghcr.io/iqbal-lab-org/cte:latest

All Docker images are listed in the packages page.

Alternatively, build your own Docker image:

sudo docker build --network=host .

Singularity

Releases include a Singularity image to download. Each release has a file called cte_vX.Y.Z.img, where X.Y.Z is the release version.

Alternatively, build your own Singularity image:

singularity build cte.simg Singularity.def

From source

Dependencies:

• Python 3
• mafft installed and in your $PATH.

Install by cloning this repository (or downloading the latest release), and running:

python3 -m pip install .