Rephrase installation

README.md

@@ -1,38 +1,48 @@
-# beacon-network-backend
+l# beacon-network-backend
 
 ###### Jakarta EE Platform 10
 The implementation is developed and deployed on the [WildFly 30.0.0](http://wildfly.org/) server and is based on Jakarta RESTful Web Services 3.0 API ([JAX-RS 3.0](https://jakarta.ee/specifications/restful-ws/3.0/)).
 
 ###### Beacon v2 Java implementation
 The implementation uses [Beacon v2 Java beacon-framework](https://github.com/elixir-europe/java-beacon-v2.api) model classes.
 
-###### SQL Database
-The Beacon Network Aggregator uses [Jakarta Persistence 3.1](https://jakarta.ee/specifications/persistence/3.1/) for logging.
-The connection is defined in [persistence.xml](https://github.com/elixir-europe/beacon-network-backend/blob/master/src/main/resources/META-INF/persistence.xml).
-Although the Aggregator may be used with any SQL database, it is configured to be used with [PostgreSQL](https://www.postgresql.org/) database.
+## Installation
 
-###### Docker Image
-This repository is configured to automatically generate docker images on release tags ('vX.Y.Z').  
-https://github.com/elixir-europe/beacon-network-backend/pkgs/container/beacon-network-backend  
-The image is based on official WildFly image that is extended with PostgreSQL driver and predeployed Beacon Network application.
-There is also a [docker-compose.yaml](https://github.com/elixir-europe/beacon-network-backend/blob/master/docker/docker-compose.yaml) receipe which provides easy deployment.
+### Docker Image (recommended)
+This repository is configured to automatically generate [docker images](https://github.com/elixir-europe/beacon-network-backend/pkgs/container/beacon-network-backend) on release tags ('vX.Y.Z'). The image is based on official WildFly image that is extended with PostgreSQL driver and predeployed Beacon Network application.
 
-###### Apache Maven build system
+To have an easy deployment, go to the [docker folder](./docker) and run [docker compose](https://docs.docker.com/compose/):
+
+```
+docker-compose up -d
+```
+
+### Manual installation
+
+#### Apache Maven build system
 The build process is based on [Apache Maven](https://maven.apache.org/).
 
 Compiling:
 ```shell
->git clone https://github.com/elixir-europe/beacon-network-backend.git
->cd beacon-network-backend
->mvn install
+git clone https://github.com/elixir-europe/beacon-network-backend.git
+cd beacon-network-backend
+mvn install
 ```
-This must create `beacon-network-v2-x.x.x.war` (**W**eb application **AR**chive) application in the `/target` directory.
+This must create `beacon-network-v2-x.x.x.war` (**W**eb application **AR**chive) application in the `/target` directory. Alternatively, you can find this file in the Barcelona Supercomputing Center's [maven repository](https://inb.bsc.es/maven/es/bsc/inb/ga4gh/beacon-network-v2/0.0.9/beacon-network-v2-0.0.9.war).
 
-###### BSC Maven Repository
-In addition to the provided docker images, artifacts are stored on the Barcelona Supercomputing Center's maven repository:  
-https://inb.bsc.es/maven/es/bsc/inb/ga4gh/beacon-network-v2/0.0.9/beacon-network-v2-0.0.9.war
+#### WilfFly server
+WildFly is a free opensource JEE server and may be easy downloaded from it's website: (http://wildfly.org/).
+The deployment is as simple:
+
+```shell
+# Copy .war file to wildfly
+cp target/beacon-network-v2-x.x.x.war $WILDFLY_HOME/standalone/deployments/
+# Run the application server
+./$WILDFLY_HOME/bin/standalone.sh
+```
+
+### Configuration
 
-###### Configuration
 There are three default configuration files in the `/BEACON-INF` directory:
 * `configuration.json` - standard beacon configuration file: [beaconConfigurationResponse.json](https://github.com/ga4gh-beacon/beacon-v2/blob/main/framework/json/responses/beaconConfigurationResponse.json)
 * `beacon-info.json` - standard beacon information file: [beaconInfoResponse.json](https://github.com/ga4gh-beacon/beacon-v2/blob/main/framework/json/responses/beaconInfoResponse.json)
@@ -45,7 +55,7 @@ The example of the `beacon-network.json`:
   "https://ega-archive.org/test-beacon-apis/cineca"
 ]
 ```
-Note that the **W**eb application **AR**chive (WAR) is just a usual ZIP file so one can edit these configurations manually without the need to rebuild the application.
+Note that the **W**eb application **AR**chive (WAR) is just a usual ZIP file so one can edit these configurations manually without the need to rebuild the application. The same with Docker, it is automatically updated with new beacons.
 
 It is also possible to define external directory for the configuration.
 ```bash
@@ -54,6 +64,12 @@ export BEACON_NETWORK_CONFIG_DIR=/wildfly/BEACON-INF
 When the `BEACON_NETWORK_CONFIG_DIR` is set, the aggregator monitors the `$BEACON_NETWORK_CONFIG_DIR/beacon-network.json` to dynamically update the configuration.  
 It also looks (but not actively monitoring) the `$BEACON_NETWORK_CONFIG_DIR/beacon-info.json` so deployers may change the beacon identifier and other metatada.
 
+### SQL Database
+
+The Beacon Network Aggregator uses [Jakarta Persistence 3.1](https://jakarta.ee/specifications/persistence/3.1/) for logging.
+The connection is defined in [persistence.xml](https://github.com/elixir-europe/beacon-network-backend/blob/master/src/main/resources/META-INF/persistence.xml).
+Although the Aggregator may be used with any SQL database, it is configured to be used with [PostgreSQL](https://www.postgresql.org/) database.
+
 The application provides simple SQL logging which level may be confirured via `BEACON_NETWORK_LOG_LEVEL` environment variable.  
 The possible values are "**NONE**", "**METADATA**", "**REQUESTS**", "**RESPONSES**", "**ALL**"
 - "**NONE**" : No logging at all.