diff --git a/README.md b/README.md index dc9f0ab5eaceca58ef5ad51534c067386f9ef63d..677c4433cb261b570656ede6705663e5db07472b 100755 --- a/README.md +++ b/README.md @@ -8,6 +8,14 @@ See `examples/example.yml` for an example of what information can be described a Each GGA environment is deployed at [https://hostname/sp/genus_species/](https://hostname/sp/genus_species/). +## Requirements + +To run the gga_load_data tools, Python 3.6 and the packages listed in [requirements.txt](./requirements.txt) are required. + +To deploy the GGA Docker services, one or multiple hosts machines are required with [Docker](https://docs.docker.com/engine/install/) installed, +and a [swarm](https://docs.docker.com/engine/swarm/swarm-tutorial) (for cluster management and orchestration). + + ## Reverse proxy and authentication Traefik is a reverse proxy which allows to direct HTTP traffic to various Docker Swarm services. @@ -71,6 +79,17 @@ $ python3 /path/to/repo/gga_load_data.py input_file.yml -c/--config config_file --main-directory $PATH (Path where to access stacks; default=current directory) ``` +## Limitations + +The stacks deployment and the data loading into Galaxy should be run separately and only once the Galaxy service is ready. +The `gga_load_data.py` script check that the Galaxy service is ready before loading the data and exit with a notification if it is not. + +The status of the Galaxy service can be checked manually with `$ 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, because of the data persistence. +In development mode only, this can be disabled by setting the variable `persist_galaxy_data` to `False` in the config file. + ## Directory tree: For every input organism, a dedicated directory is created with `gga_get_data.py`. The script creates this directory and all subdirectories required. @@ -126,23 +145,6 @@ Directory tree structure: ``` -## Current limitations - -The stacks deployment and the data loading into Galaxy should be run separately and only once the Galaxy service is ready. -The `gga_load_data.py` script check that the Galaxy service is ready before loading the data and exit with a notification if it is not. - -The status of the Galaxy service can be checked manually 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, because of the data persistence. -In development mode only, this can be disabled by setting the variable `persist_galaxy_data` to `False` in the config file. - -## Requirements - -Requires Python 3.6 - -[requirements.txt](./requirements.txt) - ## License [BSD 3-Clause](./LICENSE)