Running Jalview from the command line

Jalview can be run from the command line, and provides a range of arguments. These arguments can also be passed via .JVL files, which are opened automatically by the Jalview application when double-clicked in a file browser on Windows and OSX.

From version 2.11.2, Jalview includes a launching shell script which is the recommended way to launch an installed Jalview application from the command line. It supports all the command line arguments that Jalview has previously supported, but makes it easier to launch directly from the command line.

There are some important differences between the using the launching script and launching Jalview from its icon:

• The launching script will NOT look for updates or perform automatic updates.
• The launching script cannot open or use JVL files.

If you installed Jalview prior to version 2.11.2 you will not have had the option to add the launching shell script to your PATH. If your application has updated to 2.11.2 then the scripts will now be there, but not in your PATH. There are instructions below to add the launching shell script to your PATH if you want to do so.

• In Linux or Unix (jalview.sh)

  The installer gives 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 link (e.g. ~/bin, ~/.local/bin, ~/local/bin, ~/opt/bin). If you chose that option then you should be able to launch Jalview on the command line with the simple command

  jalview

  If 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 jalview

  or you could add /PATH_TO_JALVIEW/bin to your own $PATH as it already contains a symbolic link jalview.

• In Windows (jalview.bat, jalview.ps1)

  The installer gives 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

  jalview

  If you didn't choose that option during installation (or used an earlier version installer), you can either
  • add the \PATH_TO_JALVIEW\bin folder to your %PATH%, or
  • run the launcher script on the command line with its full path

    \PATH_TO_JALVIEW\bin\jalview.bat

    (you can leave off the .bat extension if you want).
  The jalview.bat file is a generic wrapper around the PowerShell script jalview.ps1 in 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 (jalview)

  The script you should use to launch Jalview is linked to as

  /Applications/Jalview.app/Contents/MacOS/jalview

  so you can run that command with its full path, or make your own symbolic link to there, or add that folder to your $PATH.

  If Jalview automatically updated from a version before 2.11.2 you will have to make a symbolic link to /Applications/Jalview.app/Content/Resources/app/bin/jalview.sh with the command

  ln -s /Applications/Jalview.app/Content/Resources/app/bin/jalview.sh jalview

• Future

  A future version of Jalview will include a tool to allow adding these "jalview" links to your PATH automatically.

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.

• Standard installation on Linux/Unix:

  /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

• Standard installation on Windows:

  \PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa

• OSX Application:

  open /Applications/Jalview.app --args -open /FULL/PATH/TO/myalignment.fa

  (put all the Jalview arguments after the --args parameter, and note that paths to files should be full paths from /)
  
  
• Jalview standalone executable Jar

          <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

• -Dlaf=system (default look and feel for the OS)
• -Dlaf=crossplatform (Java's Metal Look and Feel)
• -Dlaf=nimbus (Java's alternative Nimbus Look and Feel)
• -Dlaf=mac (only has an effect on OSX)
• -Dlaf=gtk (only has an effect on Linux)
• -Dlaf=metal (force Java's Metal Look and Feel, default on linux)
• -Dlaf=quaqua (macOS only. Force attempt at old macOS theme)
• -Dlaf=vaqua (macOS only. Force attempt at modern macOS theme)