Galaxy Docker Setup Guide

Docker Installation

For Ubuntu 16.04

https://docs.docker.com/engine/installation/linux/ubuntulinux/

# setup
sudo apt-get update
sudo apt-get install apt-transport-https ca-certificates
sudo apt-key adv --keyserver hkp://p80.pool.sks-keyservers.net:80 --recv-keys 58118E89F3A912897C070ADBF76221572C52609D
sudo gedit /etc/apt/sources.list.d/docker.list
# Remove any existing entries.
# Add an entry for your Ubuntu operating system.
# deb https://apt.dockerproject.org/repo ubuntu-xenial main
sudo apt-get update
sudo apt-get purge lxc-docker
apt-cache policy docker-engine
sudo apt-get update
sudo apt-get install linux-image-extra-$(uname -r) linux-image-extra-virtual

# install docker
sudo apt-get update
sudo apt-get install docker-engine

# start docker
sudo service docker start

# verify
sudo docker run hello-world

Install Galaxy Docker

service docker start
sudo usermod -aG docker $(whoami)
# log out & back in
docker run -d -p 8080:80 -p 8021:21 -p 8022:22 bgruening/galaxy-stable
# -p 8080:80 = host:container

# navigate web browser to http://127.0.0.1:8080/

Screenshot

Managing Galaxy Docker

# check the running Dockers
docker ps

# see the available images
docker images

# stop docker
docker stop <name>
# docker stop tiny_swartz

# set up the persistent storage location
GALSTOR="/home/steve/galaxy_persistent_storage"
mkdir -p "$GALSTOR"
docker run -d -p 8080:80 -v $GALSTOR:/export/ bgruening/galaxy-stable

# enter a Docker container 
docker exec -it <container name> bash
# docker exec -it mad_mahavira bash

# restart Galaxy (from outside the Docker container)
docker exec <container name> supervisorctl restart galaxy:
# docker exec mad_mahavira supervisorctl restart galaxy: