Installing on Windows
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_2_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:
In a Command Prompt, change folder to where you downloaded the file and run it with
start /wait Jalview-2_11_2_0-windows-x64-java_8.exe -c
You will be able to make the same selections found in the graphical installer.
In a Command Prompt, change folder to where you downloaded the EXE file and run it with the
Optionally you can set the installation directory with the
-dir option followed by the directory, e.g.
.\Jalview-2_11_2_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 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
sys.fileAssociation.extensions$StringArray, you must also remove or add the same number of launcher IDs (
"JALVIEW") to the
To use your own defaults
varfile run the installer with the
-varfile option and the name of the file, e.g.
.\Jalview-2_11_2_0-windows-x64-java_8.exe -q -varfile mydefaults.varfile
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