These installation notes relate to the latest installer release version
SHA256: d51887950a96d4d89071cbc6416e2f7bd742dc89e55dbb60a13f0afa2b726e5b
SHA256: 32fa6106f3afedf7e60d4b1c8006846903e4cdaa0730190cfea399ab49202c05

Installing on Unix

Graphical Installer

The Jalview SH installer for Unix should be run from the command line. It may be necessary to make the file executable.

The installer will then guide you through the installation options. In most cases we recommend accepting the default options.

If you just want to run the graphical installer, download the SH file and from a console run

bash ~/Downloads/

If you have problems, you can make the SH file executable and run it directly with:

cd ~/Downloads chmod a+rx ./ ./

TGZ File

The TGZ File is simply an archive of the application directory. You can unpack it with the command

tar -zxvf ~/Downloads/jalview-2_11_1_4-unix-java_8.tar.gz

which will create a single directory jalview with the application inside.

Whilst this installation will, when run, keep itself up to date with the latest version of Jalview, you will not benefit from some of the installer functions such as file associations.

Java 8 Required

Jalview is an application that uses a Java Runtime Environment (JRE) to run. The macOS, Windows and Linux installers bundle a JRE in the Jalview application directory so that no external JRE is required.

Since the Unix installer is more generic, bundling the correct JRE is not possible, so an external JRE will be required. Whilst the installer will run with several versions of Java, the current release of Jalview requires Java 8 (also designated Java 1.8!).

You should consult your operating system’s package management to see if a system-wide Java 8 JRE is available to install or already installed. Note that a Java Development Kit or JDK includes a complete JRE so if you have a JDK version of Java 8 installed you shouldn’t need to install a JRE as well.

A simple way to see if you have a Java 8 JRE installed is to run the command

java -version
in a console. If a Java 8 is installed you should get output like
openjdk version "1.8.0_312" OpenJDK Runtime Environment (Temurin)(build 1.8.0_312-b07) OpenJDK 64-Bit Server VM (Temurin)(build 25.312-b07, mixed mode)
that contains a version number starting with “1.8”.

If a Java 8 JRE isn’t available in the package manager, or you don’t have permissions to perform system installations, you can install a user-space JRE. We recommend the Adoptium OpenJDK packages which covers all the main OS and architeture combinations.

Other OS/architecture combinations are catered for with binary packaging of OpenJDK Java 8 at

among others.

It might be that you have a system wide Java that is not Java 8, which is being picked up by Jalview (often manifesting as a broken network). In this case you can override the system Java and point Jalview at your own Java 8 by using the INSTALL4J_JAVA_HOME_OVERRIDE environment variable. You can run Jalview from the command line like this:

INSTALL4J_JAVA_HOME_OVERRIDE=/path/to/my/java8_installation ~/opt/jalview/jalview
or for a more permanent solution, uncomment and edit the line near the top of the jalview/jalview file.

Verifying the SHA256 checksum

The download page provides a SHA256 checksum that you might want to use to verify your download. To do this in unix, open a console and use the command

sha256sum ~/Downloads/

The output checksum should match the checksum displayed on the download page.

Installing using the command line

The same SH file can be used on the command line to install Jalview if required. In this case we recommend making the SH file executable first:

cd ~/Downloads chmod a+rx ./

Console mode

In a Command Prompt, change folder to where you downloaded the file and run it with

./ -c

Unattended mode

In a Command Prompt, change folder to where you downloaded the file and run it with the -q option

./ -q

Optionally you can set the installation directory with the -dir option followed by the directory, e.g.

./ -q -dir ~/local/jalview

Note that due to Jalview’s automatic updates it is best to install Jalview in the user’s own disk space.

Changing the defaults

To set different defaults for an installation using the SH installer (most useful when using unattended mode), please read install4j Help: Response Files.

The default response file values that you might want to change for a Jalview installation look like

sys.installationDir=/Users/<user>/AppData/Local/Jalview sys.fileAssociation.extensions$StringArray="jvp","jvl","amsa","annotations,jvannotations","biojson","blc","aln","txt","fa,fasta","features,jvfeatures","gb,gbk","gff2","gff3","concise,jnet","msf","pfam","phy","pileup","pir","rnaml","mat","stk,sto" # you can also add file extensions "cif","mcif,mmcif","ent,pdb" which are not set by default sys.fileAssociation.launchers$StringArray="JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW" sys.languageId=en makeSymbolicLink$Boolean=true createDesktopLinkAction$Boolean=true
If you remove or add file extensions to the sys.fileAssociation.extensions$StringArray, you must also remove or add the same number of launcher IDs ("JALVIEW") to the sys.fileAssociation.launchers$StringArray.

To use your own defaults varfile run the installer with the -varfile option and the name of the file, e.g.

./ -q -varfile mydefaults.varfile

Further details

If you need more information about using the installer on the command line please see

or contact us on the Jalview Discussion Forum

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Thanks to ej-technologies for granting a free install4j license to the Jalview Open Source Project. Jalview's desktop installers were built with the install4j multi-platform installer builder and Gradle.