Jalview Command Line Arguments: summary
Jalview Command Line Arguments: introduction
Jalview Command Line Arguments: basic usage
Jalview Command Line Arguments: advanced usage
Jalview Command Line Arguments: argfiles
From version 2.11.3.0 Jalview processes a new set of command line arguments which allow more powerful and flexible combinations of arguments, though can also be used for very simple use cases too.
These new arguments are all accessed with a --doubledash form of
command line argument (with the one exception where simply opening one or more
files can be performed without any arguments other than the filenames).
The old command line arguments can still be used (see
the old page on command line arguments) so
existing scripts utilising them should not break.
These are now deprecated and will be removed in a future version of Jalview.
However, you cannot mix old and new style arguments, so if you use any
-singledash arguments (with the exception of -help or -h), they will all be interpreted as
old style arguments with the new --doubledash
arguments being ignored. If you have a script
that uses the old arguments without any dashes, and uses the bare-word
open then these will also be interpreted as old style arguments.
Warning! If you use command line arguments without any dashes and
don't use the bare-word argument open then all
your arguments will be interpreted as alignment files to be opened by the
new command line argument process!
To launch Jalview from the command line, see running Jalview from the command line.