Running Jalview from the command line

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.

The way that you launch Jalview from the command line depends on the platform you are on, and how it has been installed.

Standard installation on Linux/Unix:

       /PATH_TO_JALVIEW/Jalview -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://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 ~/myalignment.fa
```
(put all the Jalview arguments after the --args parameter)

Jalview standalone executable Jar

        <Path to Java home>/bin/java -jar %lt;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, then take a look at the instructions for how to setting the JVM's maximum memory.