Installation

Rock is a stand-alone Java server application. The R computation engine is handled by Rserve and therefore requires a working R environment.

Requirements

Server Hardware Requirements

Component	Requirement
CPU	Recent server-grade or high-end consumer-grade processor
Disk space	8GB or more.
Memory (RAM)	Minimum: 4GB, Recommended: >4GB

Server Software Requirements

Software	Suggested version	Download link	Usage
Java	>= 1.8.x	Java Oracle downloads	Java runtime environment
R	any version	R project	R server engine

Both Java and R must be installed on the same host.

Install

Rock is distributed as a Debian/RPM package, as a zip file and as a Docker image. The resulting installation has default configuration that makes Rock ready to be used (as soon as R is available). Once installation is done, see Configuration instructions.

Debian Package Installation

Rock is available as a Debian package from OBiBa Debian repository. To proceed installation, do as follows:

Install Debian package. Follow the instructions in the repository main page for installing Rock.
Manage Rock Service: after package installation, Rock server is running: see how to manage the Service.

RPM Package Installation

Rock is available as a RPM package from OBiBa RPM repository. To proceed installation, do as follows:

Install RPM package. Follow the instructions in the RPM repository main page for installing Rock.
Manage Rock Service: after package installation, Rock is running: see how to manage the Service.

Zip Distribution Installation

Rock is also available as a Zip file. To install Rock zip distribution, proceed as follows:

Download Rock distribution
Unzip the Rock distribution. Note that the zip file contains a root directory named rock-x.y.z-dist (where x, y and z are the major, minor and micro releases, respectively). You can copy it wherever you want. You can also rename it.
Create an ROCK_HOME environment variable
Separate Rock home from Rock distribution directories (recommended). This will facilitate subsequent upgrades.

Set-up example for Linux:

mkdir rock-home
cp -r rock-x-dist/conf rock-home
export ROCK_HOME=`pwd`/rock-home
./rock-x-dist/bin/rock

Launch Rock. This step will create/update the database schema for Rock and will start Rock: see Regular Command.

For the administrator accounts, the credentials are “administrator” as username and “password” as password. See User Directories Configuration to change it.

Docker Image Installation

OBiBa is an early adopter of the Docker technology, providing its own images from the Docker Hub repository.

See also the Rock docker images that are DataSHIELD ready: datashield/rock-base

A typical docker-compose file would be:

version: '3'
services:
  rock:
    image: obiba/rock:latest
    ports:
      - ${PORT}:8085
    environment:
      - ROCK_ADMINISTRATOR_NAME=${ROCK_ADMINISTRATOR_NAME}
      - ROCK_ADMINISTRATOR_PASSWORD=${ROCK_ADMINISTRATOR_PASSWORD}
      - ROCK_MANAGER_NAME=${ROCK_MANAGER_NAME}
      - ROCK_MANAGER_PASSWORD=${ROCK_MANAGER_PASSWORD}
      - ROCK_USER_NAME=${ROCK_USER_NAME}
      - ROCK_USER_PASSWORD=${ROCK_USER_PASSWORD}
      - ROCK_ID=${ROCK_ID}
      - ROCK_CLUSTER=${ROCK_CLUSTER}
      - ROCK_TAGS=${ROCK_TAGS}
      # for self-registration
      #- ROCK_SERVER=${ROCK_SERVER}
      #- ROCK_OPAL_SERVER=${ROCK_OPAL_SERVER}
      #- ROCK_OPAL_TOKEN=${ROCK_OPAL_TOKEN}
    volumes:
      - ${PROJECT_HOME}/rock_home:/srv

Then environment variables that are exposed by this image are:

Environment Variable	Description
`JAVA_OPTS`	JVM options.
`ROCK_ADMINISTRATOR_NAME`	Administrator user name, optional and set at first start.
`ROCK_ADMINISTRATOR_PASSWORD`	Administrator user password, optional and set at first start.
`ROCK_MANAGER_NAME`	Manager user name, optional and set at first start.
`ROCK_MANAGER_PASSWORD`	Manager user password, optional and set at first start.
`ROCK_USER_NAME`	Regular user name, optional and set at first start.
`ROCK_USER_PASSWORD`	Regular user password, optional and set at first start.
`ROCK_ID`	Rock node ID. Make sure it is unique in the cluster.
`ROCK_CLUSTER`	Cluster of R servers name. Default is “default”.
`ROCK_TAGS`	Comma separated tag names, optional. Default tag list is empty.
`ROCK_SERVER`	Self-registration: Rock server public address that will be sent to service registries (including Opal).
`ROCK_OPAL_SERVER`	Self-registration: Opal server address to register to.
`ROCK_OPAL_TOKEN`	Self-registration: Opal’s app self-registration token.

Note

When no valid user is defined, the default user setup is applied: user administrator with password password (with administrator role).

Upgrade

The upgrade procedures are handled by the application itself.

Debian Package Upgrade

If you installed Rock via the Debian package, you may update it using the command:

apt-get install rock

RPM Package Upgrade

If you installed Rock via the RPM package, you may update it using the command:

yum install rock

Zip Distribution Upgrade

Follow the Installation of Rock Zip distribution above but make sure you don’t overwrite your rock-home directory.

Execution

Server launch

Service

When Rock is installed through a Debian/RPM package, Rock server can be managed as a service.

Options for the Java Virtual Machine can be modified if Rock service needs more memory. To do this, modify the value of the environment variable JAVA_ARGS in the file /etc/default/rock.

Main actions on Rock service are: start, stop, status, restart. For more information about available actions on Rock service, type:

service rock help

The Rock service log files are located in /var/log/rock directory.

Manually

The Rock server can be launched from the command line. The environment variable ROCK_HOME needs to be setup before launching Rock manually.

Environment variable	Required	Description
`ROCK_HOME`	yes	Path to the Rock “home” directory.
`JAVA_OPTS`	no	Options for the Java Virtual Machine. For example: -Xmx1024m -XX:MaxPermSize=256m

To change the defaults update: bin/rock or bin/rock.bat

Make sure Command Environment is setup and execute the command line (bin directory is in your execution PATH)):

rock

Executing this command upgrades the Rock server and then launches it.

The Rock server log files are located in ROCK_HOME/logs directory. If the logs directory does not exist, it will be created by Rock.

Usage

To access Rock with a web browser the following urls may be used (port numbers may be different depending on HTTP Server Configuration):

http://localhost:8085 will provide a connection without encryption.

Troubleshooting

If you encounter an issue during the installation and you can’t resolve it, please report it in our Rock Issue Tracker.

Rock logs can be found in /var/log/rock. If the installation fails, always refer to this log when reporting an error.