Course materials for LIFE708

This repo contains the course materials for the LIFE708 Masters module at the University of Liverpool.

This includes a Dockerfile for the life708 container that is designed to help run the practical sessions - an automated build can be found on the Docker Hub.

Please refer here or Liverpool Vital for full instructions on accessing and setting up the course materials. The rest of this readme will describe how to run the life708 container.

• Website: Will Rowe
• Lab website: hintonlab.com
• Email: Will Rowe @ Liverpool

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

docker-machine start MACHINE-NAME

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

Pull the container image from Docker Hub:

docker pull wpmr/life708:latest

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

git clone https://github.com/will-rowe/LIFE708.git

cd LIFE708

docker build -t wpmr/life708: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 2g --name life708-$USER -v ~/Desktop/LIFE708-WORKSHOP/:/MOUNTED-VOLUME-LIFE708 wpmr/life708: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].

• --rm = makes container ephemeral

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/scripts (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)

• 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.