Galaxy templateΒΆ

The orchetrator interprets the TOSCA template and orchestrate the Galaxy deployment on the virtual machine.

Galaxy template is located here.

Input parameters are needed for each custom type used in the template:

  • Virtual hardware parameters:

    number_cpus:
  type: integer
  description: number of cpus required for the instance
  default: 1
memory_size:
  type: string
  description: ram memory required for the instance
  default: 1 GB
storage_size:
  type: string
  description: storage memory required for the instance
  default: 10 GB

  • Galaxy input paramters:

    admin_email:
  type: string
  description: email of the admin user
  default: admin@admin.com
admin_api_key:
  type: string
  description: key to access the API with admin role
  default: not_very_secret_api_key
user:
  type: string
  description: username to launch the galaxy daemon
  default: galaxy
version:
  type: string
  description: galaxy version to install
  default: master
instance_description:
  type: string
  description: galaxy instance description
  default: "INDIGO Galaxy test"
instance_key_pub:
  type: string
  description: galaxy instance ssh public key
  default: your_ssh_public_key
export_dir:
  type: string
  description: path to store galaxy data
  default: /export

  • Storage input parameters:

    galaxy_storage_type:
  type: string
  description: Storage type (Iaas Block Storage, Onedaata, Filesystem encryption)
  default: "IaaS"
userdata_provider:
  type: string
  description: default OneProvider
  default: "not_a_privder_url"
userdata_token:
  type: string
  description: Access token for onedata space
  default: "not_a_token"
userdata_space:
  type: string
  description: Onedata space
  default: "galaxy"

  • Galaxy flavor input parameters:

    flavor:
  type: string
  description: Galaxy flavor for tools installation
  default: "galaxy-no-tools"

  • Reference data input parameters, for all possible options (CernVM-FS, Onedata and download).

    reference_data:
  type: boolean
  description: Install Reference data
  default: true
refdata_dir:
  type: string
  description: path to store galaxy reference data
  default: /refdata
refdata_repository_name:
  type: string
  description: Onedata space name, CernVM-FS repository name or subdirectory downaload name
  default: 'elixir-italy.galaxy.refdata'
refdata_provider_type:
  type: string
  description: Select Reference data provider type (Onedata, CernVM-FS or download)
  default: 'onedata'
refdata_provider:
  type: string
  description: Oneprovider for reference data
  default: 'not_a_provider'
refdata_token:
  type: string
  description: Access token for reference data
  default: 'not_a_token'
refdata_cvmfs_server_url:
  type: string
  description: CernVM-FS server, replica or stratum-zero
  default: 'server_url'
refdata_cvmfs_repository_name:
  type: string
  description: Reference data CernVM-FS repository name
  default: 'not_a_cvmfs_repository_name'
refdata_cvmfs_key_file:
  type: string
  description: CernVM-FS public key
  default: 'not_a_key'
refdata_cvmfs_proxy_url:
  type: string
  description: CernVM-FS proxy url
  default: 'DIRECT'
refdata_cvmfs_proxy_port:
  type: integer
  description: CernVM-FS proxy port
  default: 80

Input parameters are passed to the corresponding ansible roles, through custom type call:

galaxy:
  type: tosca.nodes.indigo.GalaxyPortalAndStorage
  properties:
    os_storage: { get_input: galaxy_storage_type }
    token: { get_input: userdata_token }
    provider: { get_input: userdata_provider }
    space: { get_input: userdata_space }
    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 }
  requirements:
    - lrms: local_lrms

galaxy_tools:
  type: tosca.nodes.indigo.GalaxyShedTool
  properties:
    flavor: { get_input: flavor }
    admin_api_key: { get_input: admin_api_key }
  requirements:
    - host: galaxy

galaxy_refdata:
  type: tosca.nodes.indigo.GalaxyReferenceData
  properties:
    reference_data: { get_input: reference_data }
    refdata_dir: { get_input: refdata_dir }
    flavor: { get_input: flavor }
    refdata_repository_name: { get_input: refdata_repository_name }
    refdata_provider_type: { get_input: refdata_provider_type }
    refdata_provider: { get_input: refdata_provider }
    refdata_token: { get_input: refdata_token }
    refdata_cvmfs_server_url: { get_input: refdata_cvmfs_server_url }
    refdata_cvmfs_repository_name: { get_input: refdata_cvmfs_repository_name }
    refdata_cvmfs_key_file: { get_input: refdata_cvmfs_key_file }
    refdata_cvmfs_proxy_url: { get_input: refdata_cvmfs_proxy_url }
    refdata_cvmfs_proxy_port: { get_input: refdata_cvmfs_proxy_port }
  requirements:
    - host: galaxy
    - dependency: galaxy_tools

Note

Note that Reference data custom type needs Galaxy installed to the ost host: galaxy, but depends on galaxy tools dependency: galaxy_tools since it has to check installed and missing tools.

Finally we have virtual hardware customization:

host:
 properties:
   num_cpus: { get_input: number_cpus }
   mem_size: { get_input: memory_size }

Image selection:

os:
  properties:
    type: linux
    distribution: centos
    version: 7.2
    image: indigodatacloudapps/galaxy

And Storage configuration, which takes the export_dir input for the mount point and storage_size input allowing for storage size customization.

- 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 }