Deploying a Galaxy server via Ansible roles.

readme.md

Retrieve requirements.yml file and install all the roles with:

ansible-galaxy install -r requirements.yml -p roles

Create an inventory file such as the following

[my-galaxy-server]
129.114.18.39 ansible_ssh_private_key_file=key_pair.pem ansible_ssh_user=eafgan  # Jetstream via Atmo

If Ansible 2.1.0+ is installed on the host, before running the playbook, download ansible.cfg file to the same dir as the playbook. Run the playbook with

ansible-playbook -i inventory playbook.yml

ansible.cfg

[defaults]
allow_world_readable_tmpfiles=True
callback_whitelist = profile_tasks

playbook.yml

- hosts: my-galaxy-server
  become: yes
  become_user: root
  vars:
    galaxyFS_base_dir: /opt/galaxy
    galaxy_server_dir: "{{ galaxyFS_base_dir}}/galaxy-app"
    galaxy_mutable_config_dir: "{{ galaxyFS_base_dir }}/config"
    galaxy_user_name: galaxy
    galaxy_db_port: 5432
    galaxy_config_dir: "{{ galaxy_server_dir }}/config"
    galaxy_shed_tools_dir: "{{ galaxyFS_base_dir }}/shed_tools"
  roles:
    - name: galaxy-os
      postgres_user_uid: 1110
      install_maintainance_packages: no
      configure_docker: no
    - name: galaxy-nginx
    - name: galaxy-psql
      postgresql_conf:
        port: "{{ galaxy_db_port }}"
    - name: galaxy-psql-objects
      become_user: postgres
      postgresql_objects_port: "{{ galaxy_db_port }}"
      postgresql_objects_users:
        - name: galaxy
          role_attr_flags: CREATEDB,LOGIN
          password: gxydbpwd
        - name: galaxyftp
          password: gxyftppwd
          role_attr_flags: LOGIN
      postgresql_objects_databases:
        - name: galaxy
          owner: galaxy
    - name: bash_command
      cmd: 'mkdir -p /opt/galaxy/galaxy-app'
    - name: bash_command
      cmd: 'chown -R galaxy:galaxy /opt/galaxy'
    - name: galaxy
      become_user: galaxy
      galaxy_vcs: git
      galaxy_changeset_id: release_16.04
      galaxy_config:
        "server:main":
          port: 8080
          host: 127.0.0.1
        "app:main":
          admin_users: cloud@galaxyproject.org
          database_connection: postgresql://{{ galaxy_user_name }}:gxydbpwd@localhost:{{ galaxy_db_port }}/galaxy
          install_database_connection: sqlite:///{{ galaxy_mutable_config_dir }}/galaxy_install_db.sqlite?isolation_level=IMMEDIATE
          nginx_x_accel_redirect_base: /_x_accel_redirect
          nginx_upload_store: "{{ galaxyFS_base_dir }}/upload_store"
          nginx_upload_path: /_upload
          len_file_path: "{{ galaxy_mutable_config_dir }}/len"
          builds_file_path: "{{ galaxy_server_dir }}/tool-data/shared/ucsc/builds.txt"
        "filter:gzip":
          use: egg:Paste#gzip
        "filter:proxy-prefix":
          use: egg:PasteDeploy#prefix
          prefix: /galaxy
      # galaxy_mutable_configs:
      #   - src: "{{ galaxy_server_dir }}/config/migrated_tools_conf.xml.sample"
      #     dest: "{{ galaxy_config['app:main']['migrated_tools_config'] if galaxy_config is defined and 'app:main' in galaxy_config and 'migrated_tools_config' in galaxy_config['app:main'] else galaxy_config_default['app:main']['migrated_tools_config'] }}"
      #   - src: "{{ galaxy_server_dir }}/config/shed_data_manager_conf.xml.sample"
      #     dest: "{{ galaxy_config['app:main']['shed_data_manager_config_file'] if galaxy_config is defined and 'app:main' in galaxy_config and 'shed_data_manager_config_file' in galaxy_config['app:main'] else galaxy_config_default['app:main']['shed_data_manager_config_file'] }}"
      #   - src: "{{ galaxy_server_dir }}/config/shed_tool_data_table_conf.xml.sample"
      #     dest: "{{ galaxy_config['app:main']['shed_tool_data_table_config'] if galaxy_config is defined and 'app:main' in galaxy_config and 'shed_tool_data_table_config' in galaxy_config['app:main'] else galaxy_config_default['app:main']['shed_tool_data_table_config'] }}"
      #   - src: "{{ galaxy_server_dir }}/config/datatypes_conf.xml.sample"
      #     dest: "{{ galaxy_config['app:main']['datatypes_config_file'] if galaxy_config is defined and 'app:main' in galaxy_config and 'datatypes_config_file' in galaxy_config['app:main'] else galaxy_config_default['app:main']['datatypes_config_file'] }}"
      #   - src: "{{ galaxy_server_dir }}/config/tool_data_table_conf.xml.sample"
      #     dest: "{{ galaxy_config['app:main']['tool_data_table_config_path'] }}"
      #   - src: "{{ galaxy_server_dir }}/config/tool_conf.xml.sample"
      #     dest: "{{ galaxy_config_dir }}/tool_conf.xml"
    - name: trackster
      become_user: galaxy
    # - name: galaxy-tools
    #   galaxy_tools_galaxy_instance_url: ''
    #   galaxy_tools_api_key: ''
    #   galaxy_tools_tool_list_files: ['tool_list.yaml.sample']  # Copy this file to root dir

requirements.yml

- src: https://github.com/galaxyproject/ansible-galaxy-os
  name: galaxy-os
- src: https://github.com/galaxyproject/ansible-nginx
  name: galaxy-nginx
- src: https://github.com/galaxyproject/ansible-postgresql
  name: galaxy-psql
- src: https://github.com/natefoo/ansible-postgresql-objects
  name: galaxy-psql-objects
- src: https://github.com/galaxyproject/ansible-galaxy
  name: galaxy
- src: https://github.com/galaxyproject/ansible-trackster
  name: trackster
- src: https://github.com/dkreuer/ansible-role-bash-cmd
  name: bash_command
  version: patch-1
- src: https://github.com/galaxyproject/ansible-galaxy-tools
  name: galaxy-tools