Whilst the current release versions (2.11.1.*) of the Jalview installers run with a bundled Java 1.8 runtime environment, Jalview development is using Java 11 (a much more recent LTS version of Java), but is maintaining support for Java 1.8 especially for the current release versions.
This means that Jalview can run using Java 11 (and in the not-too-distant future will probably drop support for Java 1.8). There are some necessary small but significant differences in the way that Jalview is packaged for Java 1.8 and Java 11 which means it is not easy to run a Java 1.8 version using Java 11, but there are (at least) three easy ways in which you can obtain a version of Jalview to run in Java 11:
- Jalview Develop application: This is the development version of Jalview packaged as an application installer separate from the release version of Jalview. It uses a recent build of the "develop" branch of Jalview, which will include features and functionality that have not yet made it into the more stable release version. It will also auto-update like the release version when we deem the develop branch to be stable enough and want to add in some newer features. Whilst Jalview Develop should be relatively stable (it's not a nightly release) the newer features might not have been extensively tested (e.g. on all operating systems) as they would be before going into the usual release version. If you do find any problems then we encourage you to report this to us.
Note that the Jalview Develop application comes with a Java 11 runtime bundled in the application so no other software is required.
Jalview Develop is described at https://www.jalview.org/development/development-builds/ and downloadable from https://www.jalview.org/getdown/install4j/develop/.
- An unsupported Java 11 installer of the current release version of Jalview can be downloaded from https://www.jalview.org/getdown/release/install4j/11/.
Like Jalview Develop this is an installer with a Java 11 runtime bundled with the application. It will however clash with the supported Java 1.8 release version of Jalview if you have that installed as well.
- Jalview executable jar file: This is an all-in-one jar file that can be run very simply. As there is no installer it does not create the file associations, or automatically update itself, like the Jalview release or develop versions. It also has no bundled Java 11 runtime so you will need to install this separately either through your OS package manager, or via a third party Java 11 installation. We recommend (and use) the Java runtimes from AdoptOpenJDK.
You can download the 126.96.36.199 Java 11 release version of the Jalview executable jar from https://www.jalview.org/getdown/release/jalview-all-188.8.131.52-j11.jar (in general, look for the executable jar link on the download page, and change the "j8" in the URL to "j11").
To run the executable jar you just need to run:
java -jar jalview-all-VERSION-j11.jar
with your Java 11 runtime java. You might even be able to launch it by double-clicking on the jar file in a file manager!