Installation

Conda

The easiest way to obtain contigtax is via conda:

conda install -c bioconda contigtax

Docker

contigtax can also be run through a Docker container:

# Pull the image
docker pull nbisweden/contigtax
# Run a container and mounting the current directory inside the container
docker run --rm -v $(pwd):/work nbisweden/contigtax

Now you can run contigtax as you would normally by appending the commands to the end of the docker run ... call, e.g.:

docker run --rm -v $(pwd):/work nbisweden/contigtax download taxonomy

GitHub

You can also clone the GitHub repo and make sure to install the following dependencies:

  - python (>=3.5)
  - diamond
  - biopython
  - ete3
  - pandas
  - tqdm

Then run:

python setup.py install