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Installation
John Sundh edited this page Nov 25, 2020
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The easiest way to obtain contigtax is via conda:
conda install -c bioconda contigtax
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
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