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