Since Jalview 2.11.4.0 (September 2024) Jalview’s desktop installers are now able to install Jalview into shared space, with automatic updates being downloaded into users’ storage space.

For macOS, Windows, Linux and Unix the same installers found on the normal download pages can be used, although for macOS there is an installation script below that allows extra configuration steps to give a better experience for users.

User-space updates

When a new installation of Jalview is run it will assume it cannot be written to by the launching user, so will store the updatable components of Jalview (which amounts to about 55MB) in a user-space location for that user. The default location varies depending on the OS:

where HASH is an 8-character SHA256 hash of the installation folder (to distinguish between multiple installations).

Disabling or changing this default behaviour can be done at the installation stage (see Advanced options), or later.

Advanced options

The Windows and Linux installer now has an Advanced options section which we recommend leaving unchanged as the default behaviour should work well for nearly all systems. If you have a particular need to alter them then select the Enable advanced options for system installation checkbox to show the options.

• Allow user-space updates for Jalview components

This option is on by default. If you uncheck this box, and leave Allow installation updates for Jalview components unchecked, then no updates will occur. We strongly recommend not configuring Jalview like this since updates often fix critical problems or changes with either Jalview or the online services it uses (which are prone to change).

• Customise the user-space path

This is only enabled when Allow user-space updates is enabled. You can enter a template for an alternative path for user-space updates to be downloaded to. There are several substitutions that will be made to the template, and you must include at least one:

e.g. -u /tmp/jalview-desktop/%u will set the user-space updates to install in /tmp/jalview-desktop/username/jalview/HASH/app .

There are commented instructions in the file to change the settings.

• Allow installation updates for Jalview components

This option is only enabled when Allow user-space updates is disabled. If you select this checkbox then Jalview will try and update components in the installation folder. This will fail for users who do not have permissions to write in that folder. You probably don’t want to choose this, but it replicates Jalview’s update behaviour prior to version 2.11.4.0 so is included for potential backward compatibility.

Changing advanced options after installation

The advanced options are stored as properties in a file within the Jalview installation.

On macOS this file is vmoptions.txt in the Contents directory of the App bundle, e.g. /Applications/Jalview.app/Contents/vmoptions.txt .

On all other systems the file is jalviewg.vmoptions in the installation directory, e.g. /opt/jalview/jalviewg.vmoptions or C:\Program Files\Jalview\jalviewg.vmoptions .

Specific OS instructions

The installers are made easy to use for a (sensible) default installation, if you need to adjust any settings we have more specific instructions for using the Administrator mode installers for different OSes.