A Docker container that runs bioinformatics software.
Biodock was created for bioinformatic analysis at the Hinton Lab.
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
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
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[:<options>]. The comma-delimited
optionsare [rw|ro], [z|Z], [[r]shared|[r]slave|[r]private], and [nocopy].
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)
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.