galaxy_docker.yaml

tosca_definitions_version: tosca_simple_yaml_1_0

imports:
  - indigo_custom_types: https://raw.githubusercontent.com/mtangaro/tosca-types/master/custom_types.yaml

description: >
  TOSCA test for launching a Galaxy Server also configuring the bowtie2
  tool using Galaxy Tool Shed.

topology_template:
  inputs:
    instance_flavor:
      type: string
      description: instance flavor (num_cpu, memory, disk)
      default: m1.medium
    storage_size:
      type: string
      description: storage memory required for the instance
      default: 50 GB      

    admin_email:
      type: string
      description: email of the admin user
      default: ma.tangaro@gmail.com
    admin_api_key:
      type: string
      description: key to access the API with admin role
      default: GALAXY_ADMIN_API_KEY
    user:
      type: string
      description: username to launch the galaxy daemon
      default: galaxy
    version:
      type: string
      description: galaxy version to install
      default: release_18.05
    instance_description:
      type: string
      description: galaxy instance description
      default: "INDIGO Galaxy test"
    instance_key_pub:
      type: string
      description: galaxy instance ssh public key
      default: 'ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQDrm8mxOuqwP5XTHf685V9rqRXXg41F4isJvRr4h3MPDs8PgqZBzzjxEFyGpJ/Rgg4ACesGBZy+CbVVGtOveltKvgkpzyHIrh+vMay9z82eK2LMZEfmEPgw1BHdRifPZ1Qb7Zmj1nRk1EMWoNvbBxEc3/MSorWb+2SVMs+42EZ7QxavBmsU7zNU0Nd0e1xiqJ00VDWMnXullp/ieR9M4/XsSlS3oqxsxkAbY3eQYVMsnh64oiRw3lpYBkPyNtC/VSL5Cqig3CMaiK9AW8FjP1GwwqoMjL0H0Mkr0fY8eSSQ9Tcy5AqyaiPn7tmG0fSeNOFwxGkTzrujqlCiOkRSM1Yj marco@MacBook-Pro-di-Marco.local'
    export_dir:
      type: string
      description: path to store galaxy data
      default: /export

    storage_encryption:
      type: boolean
      description: Enable storage encryption using Vault to store secrets and LUKS to encrypt
      default: False
      required: true
    vault_url:
      type: string
      description: Hashicorp Vault server url
      default: "https://cloud-90-147-75-223.cloud.ba.infn.it:8200"
      required: false
    vault_wrapping_token:
      type: string
      description: Vault Wrapping token to write secret
      default: not_a_wrapping_token
      required: false
    vault_secret_path:
      type: string
      description: Vault path to store secret
      default: "subject/depuuid"
      required: false
    vault_secret_key:
      type: string
      description: Vault secret key name
      default: secret
      required: false
    iam_client_id:
      type: string
      description:
      default: iam_client_id_for_luks_client
      required: false
    iam_client_secret:
      type: string
      description:
      default: iam_secret_for_luks_client
      required: false

    flavor:
      type: string
      description: Galaxy flavor for tools installation
      default: "bgruening/galaxy-stable"

    reference_data:
      type: boolean
      description: Install Reference data
      default: true

 
  node_templates:

    galaxy:
      type: tosca.nodes.indigo.GalaxyPortalDocker
      properties:
        storage_encryption: { get_input: storage_encryption }
        vault_url: { get_input: vault_url }
        vault_wrapping_token: { get_input: vault_wrapping_token }
        vault_secret_path: { get_input: vault_secret_path }
        vault_secret_key: { get_input: vault_secret_key }
        iam_client_id: { get_input: iam_client_id }
        iam_client_secret: { get_input: iam_client_id }
        admin_email: { get_input: admin_email }
        admin_api_key: { get_input: admin_api_key }
        version: { get_input: version }
        instance_description: { get_input: instance_description }
        instance_key_pub: { get_input: instance_key_pub }
        export_dir: { get_input: export_dir }
        flavor: { get_input: flavor }
      requirements:
        - lrms: local_lrms

    # type to describe a Galaxy not using any LRMS but using the local system
    local_lrms:
      type: tosca.nodes.indigo.LRMS.FrontEnd.Local
      requirements:
        - host: galaxy_server
 
    galaxy_server:
      type: tosca.nodes.indigo.Compute
      capabilities:
        endpoint:
          properties:
            network_name: PUBLIC
            #private_ip: false
            ports:
              http_port:
                protocol: tcp
                source: 80
              ftp_port:
                protocol: tcp
                source: 21
              ftp_passive:
                protocol: tcp
                source_range: [ 30000, 30009 ]
        # Host container properties
        host:
         properties:
           instance_type: { get_input: instance_flavor }
        # Guest Operating System properties
        os:
          properties:
            #image: ost://cloud.recas.ba.infn.it/60dfe164-c9f6-4ed0-a63b-c03eea75a552(image centos RECAS)
            image: ost://keystone.cloud.garrservices.it/426bee0c-8a7a-4db8-a248-f151891de4a9 
      requirements:
        # contextually this can only be a relationship type
        - local_storage:
            # capability is provided by Compute Node Type
            node: my_block_storage
            capability: tosca.capabilities.Attachment
            relationship:
              type: tosca.relationships.AttachesTo
              properties:
                location: { get_input: export_dir }
                device: hdb

    my_block_storage:
      type: tosca.nodes.BlockStorage
      properties:
        size: { get_input: storage_size }

  outputs:
    endpoint:
      value: { concat: [ 'http://', get_attribute: [ galaxy_server, public_address, 0 ], '/galaxy' ] }
    node_ip:
      value: { get_attribute: [ galaxy_server, public_address, 0 ] }