gga_load_data

The gga_load_data tools enable automated deployment of GMOD visualisation tools (Chado, Tripal, JBrowse, Galaxy) for a bunch of genomes and datasets. They are based on the Galaxy Genome Annotation (GGA) project (https://galaxy-genome-annotation.github.io). A stack of Docker services will be deployed for each organism.

Description

Automatically generates functional GGA environments from an input yaml file describing the data. See examples/example.yml for an example of what information can be described and the correct formatting of this input file.

Each GGA environment is deployed at https://hostname/sp/genus_species/.

Traefik

Traefik is a reverse proxy which allows to direct HTTP traffic to various Docker Swarm services.

The Traefik dashboard is deployed at https://hostname/traefik/

Authentication with Authelia

The authentication layer is optional. If used, the config file needs the variables https_port, auth_hostname, authelia_config_path.

Authelia is an authentication agent, which can be plugged to an LDAP server, and that Traefik can you to check permissions to access services.

Authelia is accessed automatically by Traefik to check permissions everytime someones wants to access a page. If the user is not logged in, he is redirected to the authelia portal. Note that Authelia needs a secured connexion (no self-signed certificate) between the upstream proxy and Traefik (and https between internet and the proxy).

Steps

The "gga_load_data" tool is divided in 4 separate scripts:

• gga_init: Create directory tree for organisms and deploy stacks for the input organisms as well as Traefik and optionally Authelia stacks
• gga_get_data: Create src_data directory tree for organisms and copy datasets for the input organisms into the organisms directory tree
• gga_load_data: Load the datasets of the input organisms into their Galaxy library
• run_workflow_phaeoexplorer: Remotely run a custom workflow in Galaxy, proposed as an "example script" to take inspiration from as workflow parameters are specific to Phaeoexplorer data

Usage:

The scripts all take one mandatory input file that describes the species and their associated data (see examples/example.yml). Every dataset path in this file must be an absolute path.

You must also fill in a config file containing sensitive variables (Galaxy and Tripal passwords, etc..) that the script will read to create the different services and to access the Galaxy container. By default, the config file inside the repository root will be used if none is precised in the command line. An example of this config file is available in the examples folder.

The input file and config file have to be the same for all scripts!

• Deploy stacks part:

$ python3 /path/to/repo/gga_init.py your_input_file.yml -c/--config your_config_file [-v/--verbose] [OPTIONS]
		--main-directory $PATH (Path where to create/update stacks; default=current directory)
		--force-traefik (If specified, will overwrite traefik and authelia files; default=False)

• Copy source data file:

$ python3 /path/to/repo/gga_get_data.py your_input_file.yml [-v/--verbose] [OPTIONS]
		--main-directory $PATH (Path where to access stacks; default=current directory)

• Load data in Galaxy library and prepare Galaxy instance:

$ python3 /path/to/repo/gga_load_data.py your_input_file.yml -c/--config your_config_file [-v/--verbose]
		--main-directory $PATH (Path where to access stacks; default=current directory)

• Run a workflow in galaxy:

$ python3 /path/to/repo/gga_load_data.py your_input_file.yml -c/--config your_config_file --workflow /path/to/workflow.ga [-v/--verbose] [OPTIONS]
		--workflow $WORKFLOW (Path to the workflow to run in galaxy. A couple of preset workflows are available in the "workflows" folder of the repository)
		--main-directory $PATH (Path where to access stacks; default=current directory)

Directory tree:

For every input organism, a dedicated directory is created with gga_get_data.py. The script will create this directory and all subdirectories required.

If the user is adding new data to a species (for example adding another strain dataset to the same species), the directory tree will be updated

Directory tree structure:

/main_directory
|
|---/genus1_species1
|   |
|   |---/blast
|   |   |---/links.yml
|   |   |---/banks.yml
|   |
|   |---/nginx
|   |   |---/conf
|   |       |---/default.conf
|   |
|   |---/blast
|   |   |---/banks.yml
|   |   |---/links.yml
|   |
|   |---/docker_data  # Data used internally by docker (do not delete!)
|   |
|   |---/src_data
|   |	|---/genome
|   | 	|	|---/genus1_species1_strain_sex
|   |   |       |---/vX.X
|   |   |        	|---/vX.X.fasta
|   |   |
|   |   |---/annotation
|   |	|   |---/genus1_species1_strain_sex
|   |   |       |---/OGSX.X
|   |   |           |---/OGSX.X.gff
|   |   |           |---/OGSX.X_pep.fasta
|   |   |           |---/OGSX.X_transcripts.fasta
|   |   |
|   |   |---/tracks
|   |    	|---/genus1_species1_strain_sex
|   |
|   |---/apollo
|   |   |---/annotation_groups.tsv
|   |
|   |---/docker-compose.yml
|   |
|---/traefik
    |---/docker-compose.yml
    |---/authelia
	    |---/users.yml
	    |---/configuration.yml

Current limitations

The stacks deployment and the data loading into Galaxy should hence be run separately and only once the Galaxy service is ready. The gga_load_data.py script will check that the Galaxy service is ready before loading the data and will exit with a notification if it is not.

You can check the status of the Galaxy service with $ docker service logs -f genus_species_galaxy or ./serexec genus_species_galaxy supervisorctl status.

When deploying the stack of services, the Galaxy service can take a long time to be ready. This is due to the Galaxy container preparing a persistent location for the container data. In development mode only, this can be bypassed by setting the variable persist_galaxy_data to False in the config file.

Requirements

Requires Python 3.6

requirements.txt

License

BSD 3-Clause

Acknowledgments

Anthony Bretaudeau

Matéo Boudet