Builtin Configuration

Every software package has allow the user to configure certain aspects of its behavior. Usually the user can set parameters for a number of functions and the program will store them in a configuration file and load those parameters when the user starts up the program next time. The software will therefore remember the values of those configuration parameters.

Image has a number of configuration parameters which shouldn't be changed by the user once the software package has been installed. Those parameters dictate how Image will invoke external programs that perform the real number-crunching gel analysis.

The approach adopted for version 3.10 was to hardwire those parameters into the Image executable (the im3 program). This approach differs from the method of using different config-files for different setups and means that a different executable has to be run for each different setup. The main advantage of this approach is that full pathnames may be specified removing the dependence on the particular user's environment, i.e. $PATH, when resolving the actual location of the external programs.

The built-in parameters can easily be changed to create a new executable with different parameters, but typically this would be done once at installation by the systems administrator or the local maintainer of the Image software.

The configurable parameters

These are the names of the parameters, which are hard-wired into an Image executable of version 3.10a. The list may be extended in future versions. A blank value turns off the particular feature or function.

help_directory
Path of the directory containing these help-pages. Should be an absolute path (start with '/') and also end with a '/' character. For example /usr/local/image/help/
imageconversion
Configures the image conversion from the raw scanned image to the hidump image which can be displayed by Image.
lanetracking
Configures the command that performs the lanetracking
Its results are displayed and can be edited in Step 2
bandcalling
Configures the command that performs the band calling. Its results are displayed and can be edited in Step 3
markerlocking
Configures the command that performs the markerlocking. Its results are used in Step 4.
gelfinalisation
Configures the command that performs the gelfinalisation, which combines the results of the gel analysis into data-files for further analysis
geltransfer
Configures the script to perform the gel transfer, that transfers the data-files from the gelfinalisation step to the database or software used to do further analysis on the output of Image.
importclonenames
Can be configured to run a command to import clone names from the output of an external program. This can save typing them in one-by-one in Step 3.
nearlinerestore
Can be configured to restore gels that have been nearlined to conserve diskspace. Only used for large-scale mapping projects.

To see what the current settings are just run im3, the value of each parameter is output to the window in which image was started. You will notice that the default settings of these parameters include command line arguments of the form $name, i.e. $raw-imagefile, these are replaced by the corresponding value for the current gel at run time. All the information about the current gel is stored in the gelinfo-file only data in this file is available for use as command line arguments in the parameter values.

How to change the parameters

The tool image_configure that is provided with the distribution provides an easy way to change the parameter values that are stored in the particular executable program that is to be run by the users. Note, that the names of the possible parameter and their use is hardwired into the program code and it may vary slightly depending on the version of the program you're using. The system overview graphic will show at which stage in the gel analysis a particular configuration is used and the help-pages linked from that page will explain how.

The image_configure program is run in the command shell:

Usage :

image_configure <input> <output>

The input file is the im3-binary as contained in the distribution package, and the output file is the path/filename of the new binary which will contain the new parameter values. When the program is run each configurable parameter is presented in turn, together with it's current value. If the current value is correct just hit enter, otherwise input the required value.

Note: To enter a blank value, which disables a particular feature or function, you must enter atleast one space.

If you want to continue running image as im3, you should move the original binary and rename the new binary im3.

Last modified : November 1999 Image 3.10

* quick link - http://q.sanger.ac.uk/ty3uqbs3