GGA cloud install role

The gga_install role creates directory tree for organisms and deploys stacks for the input organisms as well as Traefik stacks.

The gga_install role :

  • installs python requirements.

  • clones the gga_load_data repository and install some python librairies required by GGA.

  • generates a config.yml and input.yml required by gga_load_data scripts

  • runs gga_init.py scripts that deploy GGA docker stacks.

Requirements

Before to run this playbook, make sure to have a hosts and ssh.cfg files in the playbook repository. If you have execute the GGA cloud terraform role before, they are in the terraform/ folder.

Role variables

Not all variables are listed or explained in detail. For additional information about less commonly used variables, see the defaults file.

Check also the github repository at https://github.com/abims-sbr/GGA_Cloud/tree/master/roles/abims-sbr.gga_install

Required variables

Host configuration file

  • hostname: The hostname that will be used to access the application (https://hostname/sp/genus_species/), possibly with a reverse proxy redirecting the requests to the host machine with the right port (https_port).

  • proxy_ip: IP of the upstream proxy (used by Traefik).

Input species variables

The file consists in a “list” of species for which the script will have to create these stacks, load data into galaxy, run workflows

  • genus_species: Name of the organism for the directory tree structure

  • input_species:

- name : genus_species
  # Species description, leave blank if unknown or you don't want it to be used
  # These parameters are used to set up the various urls and adresses in different containers
  # The script requires at least the genus to be specified
  genus:
  species:
  sex:
  strain:
  common_name:
  origin:

  # Paths to the different datasets to copy and import into the galaxy container (as a shared library)
  # Must be absolute paths to the dataset
  genome_path:
  contig_prefix:
  transcripts_path:
  proteins_path:
  gff_path:
  interpro_path:
  orthofinder_path:
  blastp_path:
  blastx_path:

Usage

Dry mode

ansible-playbook playbook_gga_install.yml --check

Real mode

ansible-playbook playbook_gga_install.yml