SEEK Virtual Machine ( version 0.19.1)

Getting the virtual machine image

VirtualBox is required to run the virtual machine. Version 4.1.22 or above is recommended.

The virtual machine image is built upon the linux based Ubuntu Server 12.04.3(LTS).

You can download the image using the following link: SEEK Virtual Machine 0.19.1
MD5: eac2ffbebd6622ce1a0fe393af252c37
SHA1: 2c06ac327a07988ea845180f0b6126941702ff0e

Using the virtual machine

The virtual machine can be imported into VirtualBox using File/Import Appliance. Browse to the downloaded file and follow the instructions. Once the machine has been started there will be some startup messages, and finally you should be presented with a login prompt.

Important settings

User credentials

These are the credentials needed to login and use the virtual machine. They are not the credentials for logging into SEEK.

Username: seek
Password: seek

You should change the default password, and even better create a new user, as soon as you can.

This user has full sudo access.

Networking information

By default the virtual machine is configured to use NAT (Network Address Translation) and Port forwarding. This is neccesary where the machine is running and is unable to obtain its own IP Address on you network without registering its MAC address. This is common in many institutions.

If in your institution you are able to obtain an IP Address, or can register the virtual machines network interface MAC address you can switch to a Bridged Network (in the Network settings for the virtual machine) and ignore the next set of instructions.

The ports are forwarded for SSH and HTTP between 2222,3333 and 22,80 respectively.

So to ssh from the host into the machine you should use:

ssh -l seek -p 2222 localhost

and to access SEEK through a browser on the host machine:

http://localhost:3333

Should you require access to SEEK other than locally, you will need to configure additional port forwarding on the host machine.

Paths

/srv/rails/seek - the SEEK installation location

/srv/rails/seek/filestore - the filestore location

/var/backups/rdiff-backup - a 2AM nightly cronjob runs as root and backs up the database and any asset files to this location using the rdiff-backup tool. You may need to set the time on the virtual machine for this to run at the correct time for you.

Creating the Administrator account

Once you access SEEK through your browser, you first need to create an initial account that will also act as the Administrator account. Once registered you can using the "Admin" pages to set up new projects, institutions and profiles.

You will need to create a Project and Institution (that are linked together) and then add yourself to that group before you are able to upload files.

Using the admin pages you can also configure the behaviour of SEEK, including some rebranding and enabling and disabling some services, in particular PUBMED and DOI support described below.

Configuring DOI and PubMed search

To be able to support adding publications using a PubMed ID or DOI to your SEEK installation, you need to do 2 things.

  • For PubMed you simply need to add your email address under Admin->Site Configuration->Additional Settings
  • For DOI - you need to register your email address with CrossRef at http://www.crossref.org/requestaccount/ and then provide that email to SEEK under Admin->Site Configuration->Additional Settings