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.

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_4_0-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_4_0-windows-x64-java_8.exe -c

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

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_4_0-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_4_0-windows-x64-java_8.exe -q -dir "%HOMEPATH%\MyApps\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 (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 on Windows look like

# install4j response file for Jalview 2.11.4.0

# Installation location (for a non Administrator user install this should be in user-space)
#sys.installationDir=

# File associations, must be from the list given and can also include "cif","mcif,mmcif","ent,pdb"
sys.fileAssociation.extensions$StringArray="jvp","jvl","amsa","annotations,jvannotations","biojson","blc","aln","fa,fasta","features,jvfeatures","fc","gb,gbk","gff2","gff3","concise,jnet","msf","pfam","phy","pileup","pir","rnaml","mat","stk,sto"

# Create a desktop icon
createDesktopLinkAction$Boolean=false

# Add Jalview's bin to the user PATH (Windows only)
appendToPathAction$Boolean=true

# Advanced options
advancedOptions$Boolean=false

# If advancedOptions is set to true then the following apply, otherwise they are ignored and defaults will be used
allowUserDefaultAppdirUpdates$Boolean=true
allowSetUserAppdirPath$Boolean=false
userAppdirPath=
allowInstallerAppdirUpdates$Boolean=false

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

.\Jalview-2_11_4_0-windows-x64-java_8.exe -q -varfile C:\Temp\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 .

Administrator install

Installing Jalview as an Administrator user so that it can be used by all users of a Windows system is possible from Jalview 2.11.4.0 onwards. Please see Administrator install and Administrator install on Windows for more details.