merge prep

README.md

@@ -1,10 +1,19 @@
 # `odc_box`
 
-This repository hosts all you need to install an *Open Data Cube* instance as a docker container that serves a Jupyter notebook environment running a Python kernel and an R kernel. It is based on the [Cube-in-a-box](https://github.com/opendatacube/cube-in-a-box) project. The changes and additions include (i) a revised `Dockerfile`, adding instructions to install R, its upstream dependencies and connect it with the Jupyter environment, (ii) helper scripts for quick re-deploys of the container environment, (iii) a revised `README.md` and (iv) additional Python dependencies. See the commit history for all changes to the original repository.
+This repository hosts all you need to install an *Open Data Cube* instance as a docker container that serves a Jupyter notebook environment running a Python kernel and an R kernel. It is based on the [Cube-in-a-box](https://github.com/opendatacube/cube-in-a-box) project. 
+
+## Additional features
+
+* an R kernel and its upstream dependencies, initialized to connect with the Jupyter environment,
+* a pre-installed suite of R packages for spatial analysis as well as there system requirements
+* helper scripts for quick starting, stoping and re-deploying of the container environment (see below),
+* a revised `README.md` with installation instructions
+
+See the commit history for all changes to the original repository.
 
 ## Installation
 
-Make sure to have [`docker`](https://docs.docker.com/engine/install/ubuntu/#install-using-the-repository) and [`docker-compose`](https://docs.docker.com/compose/install/#install-compose-on-linux-systems) installed on your host system.
+Make sure to have [`docker`](https://docs.docker.com/engine/install/ubuntu/#install-using-the-repository) and [`docker-compose`](https://docs.docker.com/compose/install/#install-compose-on-linux-systems) installed on your host system. Depending on your host system and your `docker`/`docker_compose` installation, you might need `sudo` rights for the following steps.
 
 Clone this repository to a directory of your choice, e.g. using
 
@@ -15,13 +24,13 @@ git clone https://github.com/16EAGLE/odc_box/
 and `cd` into its main directory. To start the container (and build it the first time), run:
 
 ```
-sudo ./docker_start
+./docker_start
 ```
 
 To initialize the jupyter environment and pull Sentinel-2A example data, open a new shell and run:
 
 ```
-sudo ./docker_init
+./docker_init
 ```
 
 Wait for its completion. You may then now access your local Jupyter environment in a browser on your host machine under [http://localhost](http://localhost). Use the password `secretpassword` to authenticate.
@@ -31,16 +40,16 @@ See the notebook `Sentinel_2.ipynb` for examples. Note that you can index additi
 To stop the container, from a shell other then the one the docker container is running in, run:
 
 ```
-sudo ./docker_stop
+./docker_stop
 ```
 
 To fully clean your docker environment from images pulled for `odc_box` and to allow a fresh re-deploy, run
 
 ```
-sudo ./docker_clean
+./docker_clean
 ```
 
-before starting over. Note that with each re-deploy, a new docker volume is created containing your indexed data. You may want to prune your docker volumes from time to time, e.g. using `sudo docker volume rm $(sudo docker volume ls -q -f 'dangling=true')`. Note that this will remove **all** docker volumes, also those from other docker instances that might be running on your host system.
+before starting over. Note that with each re-deploy, a new docker volume is created containing your indexed data. You may want to prune your docker volumes from time to time, e.g. using `docker volume rm $(docker volume ls -q -f 'dangling=true')`. Note that this will remove **all** docker volumes, also those from other docker instances that might be running on your host system.
 
 
 ## Troubleshooting
@@ -50,12 +59,12 @@ before starting over. Note that with each re-deploy, a new docker volume is crea
 Error message:
 
 ```
-sudo ./docker_start
+./docker_start
 #> ERROR: for postgres  Cannot start service postgres: driver failed programming external connectivity on endpoint odc_box_postgres_1 (...): Error starting userland proxy: listen tcp4 0.0.0.0:5432: bind: address already in use
 ```
 
 Reason: The default `postgres` port `5432` seems to be used by some service (maybe `postgres`?) running on your host system.
 
-Solution: Check whether this is true by running `sudo lsof -i :5432`. You may want to kill the processes that are displayed using their associated PIDs with `kill <PID>`.
+Solution: Check whether this is true by running `lsof -i :5432`. You may want to kill the processes that are displayed using their associated PIDs with `kill <PID>`.
 
 

docker_clean

@@ -1,2 +1,3 @@
 #!/bin/bash
+docker volume rm $(docker volume ls -q -f 'dangling=true')
 docker-compose down -v --rmi all --remove-orphans