Environment variables

In comparison to previous versions, im3 uses far fewer environment variables. The pathnames of external programs are now coded into the executable program itself, to avoid the dependence on the correct $PATH environment.

The variables listed here are special to Image and associated programs, Image also heeds the usual environment variables such as $DISPLAY.

$IMTOP_DIR
The most useful variable. It defines the root directory where all gel projects are stored. This directory needs to be writable by the user running the im3 program.
Several of the external scripts used to setup the gel projects, i.e. imimport require this variable to be set.
Note : im3 will pop up a filechooser to select the top-directory interactivly if no value is supplied.
$IMSHELL_CMD
contains the command line of the shell used to start external programs. im3 uses the operating system call system(3) to launch external programs (e.g. the lanetracker). Therefore this variable gives the user or system administrator more control over the way the programs are launched.
One obvious use is the loadsharing system (LSF) and the shell /bin/lstcsh which can be configured to launch programs on remote hosts or dedicated compute servers.
All programs are launched by adding the -c commandline argument to the provided shell command and append the program name and arguments. The -c seems a standard option for all shell programs to launch the program as given on the command line.
Note : If no value is supplied the programs will be launched using the default shell command /bin/sh .
$IMHELP_DIR
The use of this variable is being phased out and has been replaced with the configuration parameter "help_directory".

Last modified : February 2000 Image 3.10

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