BIRCH - GDEmenus Hints and Tips
Background execution - Most of
the time, it is best to run commands in the background by appending the
Unix 'ampersand' (&) character to the command. Background execution
immediately frees up the GDE window for other jobs. Important: see
"insave/outsave" below.
Command line - The command
specified in itemmethod can be a very long command, with separate
steps. In many, or even most cases, it makes sense to write a script
that takes care of most of the intricacies of running your program.
That way, the only thing the itemmethod command is doing is passing
parameters to the script, and maybe displaying the output.
Comments - Use comments! (#)
Explain why you did what you did. Comments can be inserted anywhere in
the item file. You can also comment out lines for testing, or for
obsolete sections.
External environment variables
- In addition to parameters in the item file, any environment variable
in the user's environment may also be used in the command line.
File format conversion - GDE is
real convenient for the user, because the person who wrote each GDE
menu item has taken care of the headache of converting file formats.
sed and tr are the two most useful Unix commands for simple conversion,
and for working around errors in how some programs produce file
formats. Most GDE menus items call readseq to convert between different
sequence file formats.
Note that the GenBank format files produced by GDE do NOT strictly
comply with the official NCBI standard!
Help files - All help files
must be accessed through the $GDE_HELP_DIR. If you need to specify a
path to files that are not part of the main BIRCH distribution, you can
use the 'root' link,
which resides in all GDE help directories. This points to the root of
the directory tree, '/'.
So, for example, to get your GDE item to display the help file found in:
/export/data/programs/emboss/share/EMBOSS/doc/programs/html/prettyplot.html
Add the following lines to the .item file:
itemhelp:root/export/data/programs/emboss/share/EMBOSS/doc/programs/html/prettyplot.html
itemopen:gde_help_viewer.csh
insave/outsave - or not? - GDE
will automatically delete all input and output files when the command
has been executed. Although convenient, there are some drawbacks. If
the command is run in the background, GDE would delete the files as
soon as the command has been launched, not when the command is
completed. This can cause a failure of files to be read or written to
completion, which can be maddening to track down.
You can inactivate the deletion of input or output files by including
insave: or outsave in your GDE menu item. However, if you do that, your
menu item must remember to delete these temporary files as part of the
command itself.
nice - If your command uses a
lot of CPU time, or if there is a significant chance of bad input
causing an endless loop (eg. an interactive program keeps prompting for
a response) always run the command at a nice level of 4 or greater.
The shell - GDE uses the BOURNE
shell to execute commands. Therefore, your itemmethod must comply with
the syntactic quirks of the BOURNE shell.
Please send suggestions of comments
regarding this page to bfristen@shaw.ca