IceBear: Research Data Management
for Structural Biology

How to install IceBear

To install IceBear, you'll download it onto a dedicated server, run a configuration script, then be guided through the set-up process in your web browser.

Please read through the instructions before starting.

Information needed

You'll need the path to your backup storage, as well as the path to IceBear's own storage if you choose not to use the default location at /icebearstore. You can install IceBear without specifying backup storage, but you should only do this if (a) your IT department have another backup system in place, or (b) you're certain that this is a test installation that won't become a real one.

You'll also need to configure the server to use secure HTTP. In a corporate or university environment, this is almost certainly a job for your local IT professionals, who will at least need to provide an SSL certificate (and, ideally, will configure the server for you). In a stand-alone test environment, you can use LetsEncrypt's CertBot to generate an SSL certificate and configure your server to use it.

If you're configuring IceBear to import from Formulatrix imagers with Rock Maker, you will also need the following:

We recommend that you set up a dedicated database user with read-only access to the two Formulatrix databases.

System Requirements

You will need a Linux server, which you'll configure with Apache, MySQL and PHP (known collectively as a LAMP stack). The installation scripts assume that your server runs Ubuntu Server 18.04 LTS, which you can download here: https://ubuntu.com/download/server

If you don't use Ubuntu Server, you'll need to configure the server manually for IceBear using the installation scripts as a guide. You'll need PHP 7.2 or later.

IceBear itself is not a particularly heavy application, but (especially when integrated with automated imagers) it does throw a lot of images around, so you should ensure that the server has both a good network connection and several terabytes of disk space. Those terabytes will also need to be backed up somewhere!

Install Ubuntu Server according to the instructions. You don't need any special configurations here, other than your regional settings at the beginning, so just take the defaults. Remember the username and password that you set!

At the end of the process, the server will reboot.

Configuring for IceBear

Now that you have a working Ubuntu Server installation, it's time to configure it for IceBear. We will install the Apache, PHP and MySQL software, download and unpack the latest version of IceBear, and run a pre-install script. That script will configure Apache and PHP, create the IceBear database tables, and also configure and enable the firewall.

NOTE: You are responsible for the security of your server! Ask your IT department for advice.

After logging in to your server with the credentials you configured during installation, become root:

sudo su

Next, install Apache, MySQL and PHP. The easiest way to do this is with tasksel:

apt-get --assume-yes install tasksel
tasksel install lamp-server

Now download the latest version of IceBear and unpack it into the web directory:

wget https://www.icebear.fi/releases/latesticebear.tar
tar -xf latesticebear.tar -C /var/www/html/

Run the configuration script:

/var/www/html/install/install.sh

This configures Apache and PHP for IceBear, creates the IceBear database, and also creates a default storage location at /icebearstore for the images and uploaded files. Now you can finish the installation process in your web browser. But...

Please read and understand the information written out at the end of the script, in consultation with your local IT support team. In particular:

Installing IceBear

Now that the server has been mostly configured, the rest of the installation process can be completed from your web browser.

Navigate to your IceBear, for example, https://icebear.youruniversity.edu, and follow the instructions there.

You'll configure storage and backup, create a default admin account, and tell IceBear about your Formulatrix imagers, if you have them. If you do connect IceBear to your imagers, you can also import users from there automatically.