Running Jalview from the command line
Jalview can be run from the command line, and provides a range of arguments.
There are a few different ways to do this:
Jalview's command line launch script
Since version 2.11.2, the Jalview native application includes a launching shell script. This is the easiest way to launch an installed Jalview application from the command line.
To run the launch script, simply open a Terminal (or Command prompt on Windows), and type:
There are some important differences between the using the launching script and launching Jalview from its icon:
If typing 'jalview' in the terminal prompt (or windows command line)
doesn't work then you will need to add the location of the jalview
launch script to your
How you do this depends on your operating system.
In Linux or Unix (
Running the Linux installer will give you the option of adding a symbolic link to
that script in your
$PATH, if it finds a suitable place that your user can add such a
~/opt/bin). If you chose that option then
you should be able to launch Jalview on the command line with the simple command
jalviewIf you didn't choose that option during installation (or used an earlier version installer), or wish to make another symbolic link, you can link to the launching shell script with the command
ln -s /PATH_TO_JALVIEW/bin/jalview.sh jalviewor you could add
/PATH_TO_JALVIEW/binto your own
$PATHas it already contains a symbolic link
In Windows (
The Windows installer will give you the option of adding Jalview's script folder to your
%PATH% allowing you to launch Jalview
in a Command Prompt simply with the command
jalviewIf you didn't choose that option during installation (or used an earlier version installer), you can either
\PATH_TO_JALVIEW\binfolder to your
\PATH_TO_JALVIEW\bin\jalview.bat(you can leave off the
.batextension if you want).
jalview.batfile is a generic wrapper around the PowerShell script
jalview.ps1in the same folder. This PowerShell script should work with both PowerShell 5.x (which is installed by default on all modern Windows machines), and also PowerShell 6.0+ which might have been installed afterwards.
In macOS (
We don't currently provide a macOS installer program, so you will need to add the command to you path manually. The script you should use to launch Jalview is linked to as
/Applications/Jalview.app/Contents/MacOS/jalviewso you can run that command with its full path, or make your own symbolic link to there, or add that folder to your
If you cannot see the
command in the MacOS directory, then you probably have an older
Jalview installation. In that case, you should make a symbolic
link directly to the launch script with the command
ln -s /Applications/Jalview.app/Content/Resources/app/bin/jalview.sh jalviewIf this doens't work, check your installation is running Jalview 126.96.36.199 or later.
Older versions of Jalview
If you are using a version of Jalview prior to 2.11.2, you can still launch from the command line, but you will have to use a more platform specific way to launch and use command line arguments.
/PATH_TO_JALVIEW/Jalview -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal
\PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa
open /Applications/Jalview.app --args -open /FULL/PATH/TO/myalignment.fa(put all the Jalview arguments after the --args parameter, and note that all files must be specified with their full paths)
<Path to Java home>/bin/java -jar <Path to Jalview Jar>/jalview-all-1.8.jar -open myalignment.fa
If you have installed Jalview via conda or another package manager then you most likely have a 'jalview' command available in your terminal shell's default path. Alternately, if you have built Jalview from source, then take a look at the doc/building.md file included in the source distribution.
Use '-help' to get more information on the command line arguments that Jalview accepts.
Passing JVM Arguments to Jalview
If you need to modify parameters for Jalview's Java Virtual Machine, or configure system properties, then take a look at the instructions for how to setting the JVM's maximum memory.
Changing Jalview's 'Look and Feel'
If you are experiencing issues with the font size or layout of Jalview's GUI, you can try changing Jalview's 'Look and feel' by specifying a custom system property 'laf' on startup (see setting the JVM's memory for instructions on how to do this for your platform).
For the Jalview standalone executable jar, simply provide one of the property settings before the -jar argument