wpmr/biodock repository overview

⁠BIODOCK

A Docker container that runs bioinformatics software.

Biodock was created for bioinformatic analysis at the Hinton Lab.

⁠General updates

11.05.2016:   Git created.
03.06.2016:   biodock updated - GitLab and DockerHub projects are now linked, the Docker image now runs using ubuntu and contains a completely new list of software

⁠Contents

1. Running biodock

If you are on a Mac, start your Docker machine:

docker-machine start MACHINE-NAME

eval "$(docker-machine env MACHINE-NAME)"

Pull the biodock image from Docker Hub:

docker pull wpmr/biodock:latest

Alternatively, clone this git and build the biodock image from the Dockerfile:

git clone https://gitlab.com/will_rowe/biodock.git

cd biodock

docker build -t wpmr/biodock:latest .

Launch the Docker container, making sure to mount a volume (allowing you to transfer data in and out of the container):

docker run -itP -m 8g --name biodock -v /some/path/on/host/:/MOUNTED_VOLUME wpmr/biodock:latest

• -i = keep STDIN open even if not attached

• -t = allocate a pseudo-tty

• -P = publish all exposed ports to the host interfaces

• -m = memory limit (8gb)

• --name = name for container at runtime (easy to use for later exec commands)

• -v = bind mount a volume (for data transfer etc. between container and host machine). Usage-> [host-src:]container-dest[:]. The comma-delimited options are [rw|ro], [z|Z], [[r]shared|[r]slave|[r]private], and [nocopy].

1. Usage

This Docker container (and git repo) is intended to provide a standardised environment for running bioinformatics pipelines, scripts and software.

The container will launch bash by default, all software is in the path and scripts from the git repo are in /opt/SCRIPT_bin (also in path)

A few helpful commands for managing the container:

• Once exited, you can re-enter the container using the exec command:

docker exec -it [CONTAINER ID] bash

• View all containers (both running and stopped) using:

docker ps -a

• Stop or remove all containers

docker stop $(docker ps -aq)

docker rm $(docker ps -aq)

1. Notes

• The CPUs available to Docker are limited by the host machine running docker, so set the virtual machine to have the required number before running Docker.

• The Kernel scheduler will handle the resource contention in the case of multiple containers requiring multiple cores.