Release 1.0

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)