Installation: with docker

Run Pangraph CLI inside a Docker container.

Note

The following instructions assume you have Docker installed and is familiar with the basics. Explanation of Docker is out of scope of this documentation. Refer to Docker documentation if necessary.

Pull latest version of neherlab/pangraph image from DockerHub:

docker pull neherlab/pangraph

or pull a particular version

docker pull neherlab/pangraph:1

Run pangraph commands described in CLI reference or Tutorials as in following examples:

docker run -it --rm neherlab/pangraph pangraph --help

# Mount current directory to /data and run as current user
docker run -it --rm --volume="$(pwd):/data" --user="$(id -u):$(id -g)" neherlab/pangraph pangraph build /data/input.fasta -o /data/pangraph.json

Note

Don't forget to add volumes to be able to access data on the host. You might also want to run docker container as a non-root user.

Extending the image

You can base your own containers based on pangraph image and add your own software and functionality, for example:

FROM neherlab/pangraph:1

RUN sudo apt-get update && sudo apt-get install python3

COPY my-script.py /usr/bin/my-script.py

# ... remainder of your image

or you can add standalone pangraph binaries to any image:

FROM my-org/my-image

RUN curl -fsSL "https://github.com/neherlab/pangraph/releases/latest/download/pangraph-x86_64-unknown-linux-gnu" -o "/usr/bin/pangraph" && chmod +x /usr/bin/pangraph

# ... remainder of your image