- Command Line: summary
-
- Command Line: introduction
-
- Command Line: basic usage
-
- Command Line: advanced usage
-
- Command Line: argument files
-
- 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. -
- -