indigo-dc.galaxycloud_docker

This role has been developed to be used in the Laniakea project in order to run the official Galaxy Docker containers and its flavours on a Centos7 (or Ubuntu 16.04) Virtual Machine, creating Galaxy administrator user and mounting specific CernVM file system.

Galaxy customization

• User administrator creation
• Galaxy brand customization
• Anonymous login disabled
• Allow user creation
• Allow user impersonation
• CVMFS customization (default: data.galaxyproject.org)

Requirements

This ansible role supports CentOS 7 and Ubuntu 16.04 Xenial.

Minimum ansible version: 2.1.2.0

Role Variables

Main variables

galaxy_instance_description: set galaxy brand, default = "ELIXIR-IT"

export_dir: directory hosting 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 to tool_data_table_conf.xml file = '/etc/galaxy/tool_data_table_conf.xml'

Galaxy admin user creation

GALAXY_ADMIN_PASSWORD: Galaxy administrator password.

GALAXY_ADMIN_API_KEY: Galaxy administrator API KEY.

GALAXY_ADMIN_EMAIL: Galaxy administrator email.

Galaxy CVMFS role variable

refdata_cvmfs_repository_name: name of the CVMFS repository to mount on 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 mountpoint for the CVMFS server, default = "/cvmfs"

Role templates

default.local.j2: config file for CVMFS repository that will be mounted on the Galaxy Docker.

mygalaxyenv.j2: env file with the environment variables needed to configure the Galaxy Docker.

Dependencies

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

Example Playbook

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

License

Apache Licence 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