These installation notes relate to the latest installer release version 2.11.1.4
SHA256: 5d275a4c42c420ec9d13753b2e2c07a48586367aac694f7e6625cfc0553254b0

Installing on Windows

Graphical Installer

The Jalview installer for Windows can be run by double-clicking on the downloaded EXE file in a File Manager window, or launching it directly from your browser after downloading.

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

Installation on Windows
Installation on Windows

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 Windows, open a Command Prompt or Powershell and use the command

certutil -hashfile ".\Downloads\Jalview-2_11_1_4-windows-x64-java_8.exe" SHA256

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

Installing using the command line

The same EXE file can be used on the command line to install Jalview if required:

Console mode

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

start /wait Jalview-2_11_1_4-windows-x64-java_8.exe -c

You will be able to make the same selections found in the graphical installer.

Console mode install on Windows
Console mode install on Windows

Unattended mode

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

.\Jalview-2_11_1_4-windows-x64-java_8.exe -q

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

.\Jalview-2_11_1_4-windows-x64-java_8.exe -q -dir "%HOMEPATH%\MyApps\Jalview"

Unattended mode install on Windows
Unattended mode install on Windows

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 (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.

.\Jalview-2_11_1_4-windows-x64-java_8.exe -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.