Building Docker image

Install dependencies

• Install bash and make.

• Install Docker: https://docs.docker.com/get-docker/

• Optionally setup Docker so that it runs without sudo: https://docs.docker.com/engine/install/linux-postinstall/

Build Docker image locally

Run:

make docker

This will build the Docker image tagged neherlab/pangraph (more precisely neherlab/pangraph:latest). If already exists, it will replace the existing image with that tag. The build will take some time.

If completed successfully, then the image can be used right away. Refer to user documentation. Skip the "Pull Docker image" step.

Explore contents, layers and optimize image size

You could use dive tool to see what's inside an image:

dive neherlab/pangraph:<tag>

Each layer reflects FROM, COPY and RUN commands and the files that have been added to the overlay file system of the image. This can be used to find redundant files. You could then further optimize Dockerfile and make the image smaller.

Testing the image

Once the image has been built locally it can be tested by running (from the repository main folder):

docker run -it --rm \
    --volume="$(pwd):/workdir" \
    --workdir="/workdir" \
    --user="$(id -u):$(id -g)" \
    neherlab/pangraph \
    bash tests/run-cli-tests.sh

Or more simply using instructions in the Makefile:

make docker-test

This will test all the available commands, see tests/run-cli-tests.sh script.