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Indigo-dc.galaxycloud-refdata

Reference data ansible role for indigo-dc.galaxycloud. The role provides reference data using the CernVM File System and the corresponding galaxy configuration.

Requirements

To correctly configure the CernVM File System the role run the indigo-dc.cvmfs-client ansible role as dependency to install and configure the CVMFS client.

indigo-dc.cvmfs-client

Role Variables

galaxy_flavor: if different from 'galaxy-no-tools' the role will check if all tools installed using https://github.com/indigo-dc/ansible-galaxy-tools have been correctly installed. Possible galaxy_flavor values with the correspinding recipes are reported here: :doc:feat_galaxy_tools (default: galaxy-no-tools).

get_refdata: enable reference data configuration. If set to false this variable disable reference data configuration (default: true).

cvmfs variables

refdata_cvmfs_server_url: set CernVM-FS server (stratum 0 or Replica) address without 'http://' string, e.g. single ip address.

refdata_cvmfs_repository_name: set a different cvmfs repository name, overwriting the default option, which point to refdata_repository_name (e.g. elixir-italy.galaxy.refdata).

refdata_cvmfs_key_file: SSH public key to mount the repository

refdata_cvmfs_proxy_url: proxy address (default DIRECT).

refdata_cvmfs_proxy_port: proxy port (default 80).

Dependencies

For cvmfs server reference data provider, the role depends on indigo-dc.cvmfs-client role, which takes as input parameters the CernVM-FS server location details (stratum 0 address, public key and mount point).

- hosts: servers
  roles:
    - role: indigo-dc.cvmfs-client
      server_url: '90.147.102.186'
      repository_name: 'elixir-italy.galaxy.refdata'
      cvmfs_public_key: 'elixir-italy.galaxy.refdata.pub'
      proxy_url: 'DIRECT'
      proxy_port: '80'
      cvmfs_mountpoint: '/refdata'
      when:  refdata_provider_type == 'cvmfs'

Example Playbook

  • Configure Galaxy with CernVM-FS reference data volume.
- hosts: servers
  roles:
    - role: indigo-dc.galaxycloud-refdata
      galaxy_flavor: 'galaxy-no-tools'
      get_refdata: true
      refdata_cvmfs_server_url: '90.147.102.186'
      refdata_cvmfs_repository_name: 'elixir-italy.galaxy.refdata'
      refdata_cvmfs_key_file: 'elixir-italy.galaxy.refdata.pub'
      refdata_cvmfs_proxy_url: 'DIRECT'
  • Configure Galaxy with CernVM-FS reference data volume with preconfigured config.d files
- hosts: servers
  roles:
    - role: indigo-dc.galaxycloud-refdata
      galaxy_flavor: 'galaxy-no-tools'
      get_refdata: 'true'
      refdata_dir: '/cvmfs'
      refdata_cvmfs_configuration: 'cvmfs_preconfigured'
      refdata_cvmfs_repository_name: 'elixir-italy.galaxy.refdata'
      refdata_cvmfs_key_file: 'elixir-italy.galaxy.refdata.pub'

License

Apache Licence v2

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

References

Galaxy project: https://galaxyproject.org

CernVM-FS: http://cvmfs.readthedocs.io/en/stable/index.html

Author Information

Marco Tanagaro (ma.tangaro_at_ibiom.cnr.it)