Typically for interactive use of pregap4 users need type nothing more than
pregap4
. For the more inquisitive user the following command line
options are available.
-config
config_file
-
This specifies an alternative configuration file to Pregap4. The default
configuration file is named `pregap4.config'. It is valid to specify a
filename which does not yet exist. This filename will be used for both reading
and writing configurations to.
-fofn
filename
-
Specifies a file of filenames for processing. Multiple uses of
-fofn
are allowed and they are additive. The default prefix for pregap4 output files
is derived from the last specified file of filenames.
-nowin
-
-no_win
-
These are synonyms. They prevent pregap4 from displaying its graphical user
interface and force it to automatically "Run". This argument should only be
used when driving pregap4 as a batch job. It is necessary to create a valid
configuration file before using this option.
-win_compact
-
This uses a compact GUI mode with the main dialogues listed as separate tabs
in the main window. This can be made the default display style by selecting
"Compact Window Style" in the Options menus. The command line option overrides
this default.
See section Window Styles.
-win_separate
-
This uses a GUI mode using separate top level windows in a similar manner to
Gap4 and Spin. This can be made the default display style by selecting
"Separate Window Style" in the Options menus. The command line option
overrides this default.
See section Window Styles.
--
-
Indicates the end of pregap4 options. This is used in case filenames start with
a minus sign, to distinguish filenames from possible pregap4 options.
Any other arguments on the command line are assumed to be filenames. For
example the following command executes pregap4 in batch mode using
configuration file `batchX' on all files in the current directory named
something.ZTR
.
pregap4 -config batchX -nowin -- *.ZTR
The --
in the above example is to guard against the unlikely case where
*.ZTR
could match a filename starting with minus.
This page is maintained by
staden-package.
Last generated on 22 October 2002.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/pregap4_unix_13.html