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/jalview-2_11_3_3-unix-java_8.sh

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

cd ~/Downloads
chmod a+rx ./jalview-2_11_3_3-unix-java_8.sh
./jalview-2_11_3_3-unix-java_8.sh

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_3_3-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 (sometimes 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

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 cover all the main OS and architecture combinations.

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

• AdoptOpenJDK,
• Azul Zulu,
• Amazon Coretto

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

Java 11 development version

Jalview is being developed to compile and run under Java 11 as well as Java 8. This offers a number of extra benefits including better integration with macOS menus and 4k display detection in Linux. However there are some bugs in the underlying Java 11 JVM that we want to iron out before compiling the release version for Java 11.

Our “Develop” channel uses Java 11 by default. You can easily try this out with the Jalview Develop desktop application that sits alongside the release version of Jalview but uses a Java 11 JVM.

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/jalview-2_11_3_3-unix-java_8.sh

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 ./jalview-2_11_3_3-unix-java_8.sh

Console mode

In a Console or Terminal, change folder to where you downloaded the file and run it with

./jalview-2_11_3_3-unix-java_8.sh -c

Unattended mode

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

./jalview-2_11_3_3-unix-java_8.sh -q

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

./jalview-2_11_3_3-unix-java_8.sh -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

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

./jalview-2_11_3_3-unix-java_8.sh -q -varfile mydefaults.varfile

Further details

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

• install4j Help: Installer Modes
• install4j Help: Command Line Options For Generated Installers
• install4j Help: Response Files

or contact us on the Jalview Discussion Forum