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galaxy-ethercalc's Introduction

galaxy-ethercalc

Files

  • DockerFile - This file defines the build for the eschen42/ethercalc docker image.
  • etc-init.d-galaxy_docker - This file is to be copied to /etc/init.d/galaxy_docker for use in starting and stopping galaxy-compose.yml as a service.
  • galaxy-compose.yml - Start or stop Galaxy, ethercalc, and redis containers.
  • start.sh - Start galaxy-compose.yml; must be run as root.
  • stop.sh - Stop galaxy-compose.yml; must be run as root.
  • add_galaxy_users.sh - Add users galaxy and postgres to /etc/passwd and /etc/group.

Advice

Ensure that you have installed "Docker Compose" as described at https://docs.docker.com/compose/install

You definitely need to update GALAXY_CONFIG_BRAND and GALAXY_CONFIG_ADMIN_USERS in the enviroment in galaxy-compose.yml.

  environment:
    # TODO update admin user identifier(s); this is a comma-separated list
    - GALAXY_CONFIG_ADMIN_USERS=you@somedomain
    # TODO update brand
    - GALAXY_CONFIG_BRAND='unbranded W4M'

You almost definitely will want to add users galaxy and postgres:

sudo groupadd -g 1450 galaxy
sudo groupadd -g 1550 postgres
sudo useradd -d /home/galaxy -m -u 1450 -g 1450 -s /bin/bash -c "galaxy user within docker" galaxy
sudo useradd -d /home/postgres -m -u 1550 -g 1550 -s /bin/bash -c "postgres user within docker" postgres

This can be achieved by running add_galaxy_users.sh.

Note that the first time you run galaxy-compose.yml with docker-compose, it takes a long time because it has to build W4M, which takes longer than the timeout for systemctl start galaxy_docker. So, before starting the service, run start.sh as root; once the docker containers have started, run stop.sh; then systemctl start galaxy_docker should succeed.

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