@@ -6,9 +6,25 @@ They are based on the [Galaxy Genome Annotation (GGA) project](https://galaxy-ge
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@@ -6,9 +6,25 @@ They are based on the [Galaxy Genome Annotation (GGA) project](https://galaxy-ge
A stack of Docker services is deployed for each species, from an input yaml file describing the data.
A stack of Docker services is deployed for each species, 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.
See `examples/example.yml` for an example of what information can be described and the correct formatting of this input file.
The services currently deployed are:
- Chado database
- Tripal: database interface and hub to all applications
- Elasticsearch: searching service used in Tripal
- JBrowse: genome browser
- Nginx proxy: page to download the data files
- Blast (optional): BLAST interface to query the data
- Galaxy: data loading orchestrator for administrators
A GGA environment is deployed for each different species at [https://hostname/sp/genus_species/](https://hostname/sp/genus_species/).
A GGA environment is deployed for each different species at [https://hostname/sp/genus_species/](https://hostname/sp/genus_species/).
Multiple strains can have the same species and are deployed in the same GGA environment.
Multiple strains can have the same species and are deployed in the same GGA environment.
_**Figure** : Schematic representation of a set of Docker containers deployed with
GGA for typical genomes. Cuboids represent Docker containers. Hexagons represent different
sets of Docker containers. Blue arrows represent HTTP traffic. Gray arrows represent
data exchange performed using Galaxy tools. Black arrows represent data exchange
inherent in applications._
## Requirements
## Requirements
To run the gga_load_data tools, Python 3.6 and the packages listed in [requirements.txt](./requirements.txt) are required.
To run the gga_load_data tools, Python 3.6 and the packages listed in [requirements.txt](./requirements.txt) are required.
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@@ -22,8 +38,8 @@ and a [swarm](https://docs.docker.com/engine/swarm/swarm-tutorial) (for cluster
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@@ -22,8 +38,8 @@ and a [swarm](https://docs.docker.com/engine/swarm/swarm-tutorial) (for cluster
Traefik is a reverse proxy which allows to direct HTTP traffic to various Docker Swarm services.
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/](https://hostname/traefik/)
The Traefik dashboard is deployed at [https://hostname/traefik/](https://hostname/traefik/)
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 an authentication agent, which can be plugged to an LDAP server, and that Traefik can used to check permissions to access services.
The authentication layer is optional. If used, the config file needs the variables `https_port`, `authentication_domain_name`, `authelia_config_path`.
The authentication layer is optional. If used, the config file needs the variables `https_port`, `authentication_domain_name`, `authelia_config_path`, `authelia_secrets_env_path`, `authelia_db_postgres_password`.
Authelia is accessed automatically by Traefik to check permissions everytime someones wants to access a page.
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.
If the user is not logged in, he is redirected to the authelia portal.
