Using the Jalview Launch file
Downloading the Jalview Release JVL File above and opening it with an installed Jalview app will reconfigure the app so it will open up the current release version. The app will also automatically download future releases when they become available.
Remember! You only need to do this if you previously moved your Jalview application onto a different channel.
Opening JVL files
What is a Jalview Launch file?
JVL Files are special text files read by Jalview’s Desktop apps that control the way that the app launches Jalview. They also provide a way to change the update channel that the Jalview Desktop app checks. Confusingly, that means you can use any installed Jalview Desktop app (from Jalview 2.11 onwards) to launch any version of Jalview, providing there is a JVL file available.
To avoid confusion we actually provide three different Jalview Desktop apps: Jalview, Jalview Test, and Jalview Develop. Each app is configured to check one of the three Jalview update channels and download the latest verson available. If you just want to run the latest stable version of Jalview, download an installer for your platform.
Creating your own Jalview launch file
Jalview Launch (JVL) files are simply text files that contain
key=value pairs for a number of arguments that control how Jalview is launched via a Jalview Desktop App. In addition to changing the currently configured Update Channel, the JVL file can also control how much memory Jalview requests, or pass command line arguments. Unlike the update channel configuration, command line arguments and memory settings will not be remembered the next time the Jalview Desktop App is launched.
A powerful feature of the JVL file is that it can also change which part of the Jalview website Jalview looks for updates. We call this changing the “channel” that Jalview is updating from. The vast majority of users will never need to do this as Jalview installs itself using the Release channel which will keep that Jalview installation up to date with the latest stable release of Jalview.
We have several standard channels: Release, Test and Develop. These are each easily accessed using their corresponding Desktop apps: Jalview Release, Jalview Test, or Jalview Develop. Each app is configured to follow the relevant channel when launched and maintains its own configuration and user preferences.
It is also possible to switch to a specific “branch” channel that might have a feature in development, or a bugfix that needs to be tested before the code is merged to the develop or release branches. These channels are usually hosted on Jalview’s build server https://builds.jalview.org/. Lastly, old versions are archived with their own release channels and JVL files, linked via Version Archive.
Here are the main properties you might want to set:
This sets the location of the channel that Jalview will switch to (and then stay on until changed back).
e.g. the Release channel (for Java 8) is
appbase = https://www.jalview.org/getdown/release/1.8
This passes an argument to Jalview similarly to when you open Jalview using the command line. This property can be used multiple times and the arguments appear in the order they are listed in the JVL file. A full list of Jalview command line arguments can be found in the Help pages.
e.g. To open an alignment file along with a specific features and/or annotations file you could use the following JVL file (note that paths could be on your filesystem):
jalview.apparg = open
jalview.apparg = https://www.jalview.org/examples/plantfdx.fa
jalview.apparg = features
jalview.apparg = https://www.jalview.org/examples/plantfdx.features
jalview.apparg = annotations
jalview.apparg = https://www.jalview.org/examples/plantfdx.annotations
These are arguments passed to the Java JVM (not to the Jalview application).
e.g. To set the Java property
laf to “nimbus” you could use a JVL file with the line:
jvmarg = -Dlaf=nimbus
This tries to set the Java JVM memory stack to a percentage of memory available on your machine. Note that this can only work if the JVM can detect this amount (which is usually the case, but if you are using a non-standard JVM this might not work). The default is 90.
jvmmemmax work best together.
e.g. To set the memory stack to 10% of memory use:
jvmmempc = 10
This is an absolute cap on how much memory is allocated to Jalview, even if the
jvmmempc argument would assign more. If your machine’s memory has been detected, the default is 32GB. If your machine’s memory has not been detected, the default is 8GB. You can use a
t suffix to represent kilobytes, megabytes, gigabytes or terabytes.
jvmmemmax work best together.
e.g. To set a memory cap of 1.5GB use a JVL file with the line:
jvmmemmax = 1536m