indigo-dc.galaxycloud_docker

This role is made for the Laniakea project to use the official Galaxy Docker containers on a CentOS 7 (or Ubuntu 16.04) Virtual Machine. It sets up a Galaxy administrator user and connects a specific CernVM file system.

Galaxy Customization

• Create a user administrator
• Customize Galaxy branding
• Disable anonymous login
• Allow user creation
• Allow user impersonation
• Customize CVMFS (default: data.galaxyproject.org)

Requirements

This Ansible role works with CentOS 7 and Ubuntu 16.04 Xenial.

Minimum Ansible version: 2.1.2.0

Role Variables

Main Variables

galaxy_instance_description: Set the Galaxy brand, default = "ELIXIR-IT"

export_dir: Directory for Galaxy database files and Docker images, default = "/export"

galaxy_flavor: "<owner>/<docker>:<docker_flag>", Set the Galaxy Docker container, default = "bgruening/galaxy-stable:18.05"

tool_data_table_conf: Default path for tool_data_table_conf.xml file = '/etc/galaxy/tool_data_table_conf.xml'

Galaxy Admin User Creation

GALAXY_ADMIN_PASSWORD: Password for the Galaxy administrator.

GALAXY_ADMIN_API_KEY: API KEY for the Galaxy administrator.

GALAXY_ADMIN_EMAIL: Email for the Galaxy administrator.

Galaxy CVMFS Role Variables

refdata_cvmfs_repository_name: Name of the CVMFS repository to mount in the Docker container, default = "elixir-italy.covacs.refdata"

server_url: IP address or URL of the STRATUM 0 or STRATUM 1 server, default = "90.147.75.251"

cvmfs_server_url: "http://{{ server_url }}/cvmfs/{{ refdata_cvmfs_repository_name }}"

cvmfs_public_key_path: URL of the key to download, default = "/etc/cvmfs/keys"

cvmfs_public_key: "{{ refdata_cvmfs_repository_name }}.pub"

proxy_url: Proxy server or DIRECT, default = DIRECT

proxy_port: 80

cvmfs_http_proxy: "http://{{ proxy_url }}:{{ proxy_port }}"

cvmfs_mountpoint: Docker mount point for the CVMFS server, default = "/cvmfs"

Role Templates

default.local.j2: Config file for the CVMFS repository that mounts on the Galaxy Docker.

mygalaxyenv.j2: Environment file with variables to configure the Galaxy Docker.

Dependencies

indigo-dc.docker: Install Docker engine and store Docker images in the external volume (/export).

Example Playbook

- name: Minimum playbook
  hosts: localhost
  roles:
    - { role: galaxycloud_docker }
  vars:
    GALAXY_ADMIN_EMAIL: "<your@email>"

License

Apache License v2

http://www.apache.org/licenses/LICENSE-2.0

Reference

Galaxy Docker: https://github.com/bgruening/docker-galaxy-stable

Laniakea Project Documentation: https://laniakea.readthedocs.io/en/latest/

Official CVMFS Documentation: http://cvmfs.readthedocs.io/en/stable/cpt-repo.html