Requirements

Hardware

Minimum

The following will show you the minimum requirements of the BIBBOX ubuntu machine. Please note, that installing any applications within BIBBOX will require additional resources!

  • CPU cores: 1
  • Memory: 4096 MB
  • Disk space: 20 GB

Recommended for Development

For development purposes we recommend a virtual machine with the following specifications:

  • CPU cores: 4
  • Memory: 8192 MB
  • Disk space: 100 GB

Production

For production, please calculate the additional resources you will need, depending on the applications you are going to install within the BIBBOX.

Software

Installation

You have to specify a domain bibbox will be accessible in the installation script. This can be either a local domain, or a fully qualified domain name (FQDN). In case of a FQDN make sure that the DNS/proxy has wildcard domains enabled, i.e. also subdomains can be reached.

sudo git clone https://github.com/bibbox/kit-eb3kit.git /opt/bibbox-install

sudo chmod +x /opt/bibbox-install/*.sh

sudo /opt/bibbox-install/install-bibbox-local.sh -url put.here.your.domain -gui

Watch the installation scripts, sometime apt-get makes some problems.

Login and administration

You can reach the BIBBOX framework with your choosen domain in any Webbrowser, and log into with one of the five default users and the password graz2017:

  • bibboxadmin
  • admin
  • pi
  • curator
  • operator

If you want to make changes to the default configuration of the portal (e.g. change the title or logo), you need to log in as bibboxadmin.

When you enter the BIBBOX framework in commandline mode, all the components are installed under /opt/bibbox. What's going up there is described in the different componenets (github repositories). The Github repositories are structured according to the following naming conventions:

  • application-store, this repository describes all applications (applications.json) and annotated lists of application for a specific domain, called kits. Currently we provide one default kit, described in eB3kit.json.

  • KIT-.... repositories provides the blueprint how to build a "kit". A kit is a VM providing the base BIBBOX framework together with a set of predefined tools (kit.json in the applications directory), pre-loaded docker images and (reference) databases. Currently we provide one default kit: kit-eb3kit.

  • APP-.... repositories describes BIBBOX APPs. Each BIBBOX application is compodes by of offical docker images or docker images from the BIBBOX docker hub.

  • SYS-.... repositories source code running inside the virtual machine, which provides all services of the BIBBOX SaaS framework.

    • sys-bibbox-backend-liferay backend of the BIBBOX portal, based on the liferay framework. Functionality for the management of applications instances, the application store and the central user management.

    • sys-bibbox-frontend all frontend code (React libraries). They are loaded by the backend at runtime.

    • sys-activities service, for logging and synchronisation of all high level activities (installation, app delete, start/stop, etc.) running as a docker container.

    • sys-idmapping service, for mapping of internal IDs and connection to external ID systems (B2Handle, EPIC) running a a docker container.

    • sys-bibbox-vmscripts Collection of phyton scripts for management of applications, e.g. installation, port management, file management, setup script for the configuration of the portal, called after vagrant / puppet scripts are finished.

  • RES-.... repositories ressources. e.g. a common icon set for biobank applications.

Domain Migration

If you want to migrate from SOME.OLD.DOMAIN to YOUR.NEW.DOMAIN, login into your VM and make the following steps

  • Stop the apache service

sudo service apache2 stop

  • Replace all SOME.OLD.DOMAIN in the proxy files

cd /etc/apache2?

sudo cp -r sites-available sites-available-back

cd sites-available

sed -i 's/SOME.OLD.DOMAIN/YOUR.NEW.DOMAIN/g' *

sudo service apache2 start

  • Change to config for the portal

cd /etc/bibbox

sudo service liferay stop

sudo sed -i 's/SOME.OLD.DOMAIN/YOUR.NEW.DOMAIN/g' bibbox.cfg

sudo service liferay start