docs/docker.md

In matsengrp/sumrep: Summary statistics for B cell receptor (BCR) repertoires

Building sumrep using Docker

sumrep can be built using Docker, a framework which allows for a clean installation of sumrep and all of its dependencies in an isolated, controlled environment. You can learn more about using Docker in this very nice vignette by Erick Matsen. Follow either of the two steps below to build and run a Docker image for sumrep.

Using a pre-built image of sumrep

You can find the latest build of sumrep in Dockerhub.

Run the command

docker pull brandenolson/sumrep

to pull the image from Dockerhub. Once this is finished, run

docker run -it brandenolson/sumrep

to start an interactive container in which sumrep as well as all of its required and optional dependencies are available.

Building sumrep manually

sumrep can be built manually according to the Dockerfile. Simply run the following command in the directory of the Docker file to build the Docker image:

docker build -t sumrep .

(Docker by default tries to cache things when repeatedly doing a build; you can run a clean build via docker build --no-cache -t sumrep .)

Once the build is finished, run

docker run -it sumrep

to start an interactive container in which sumrep as well as all of its required and optional dependencies are available.

Linking a local directory to the sumrep Docker image

If you wish to link a local directory at /path/to/local/dir to a corresponding directory in the Docker image at /path/to/docker/dir, simply run

docker run -it -v /path/to/local/dir:/path/to/docker/dir brandenolson/sumrep

(If you built manually, replace brandenolson/sumrep with sumrep)

matsengrp/sumrep documentation built on Oct. 12, 2022, 4:09 p.m.