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Geltransfer configuration

This configuration keyword defines the program that transfers the data-files from the gelfinalisation step to the database or software used to do further analysis on the output of Image.

This program is called after gelfinalisation when the gel is finished (by stepping forward) in step 4 using the right-arrow button.

Command line arguments

The configuration of this command and the command itself is totally up to the administrator and depends on the nature of the further analysis intended for the project in hand.

Traditionally the command is a shell/perl-script written by the administrator which transfers the gel/ bands/ sizes files or their contents to a database. If no such transfer is required this parameter should be configured as a blank text to disable the execution of a transfer command.

1. configuring transfer to fpc

The image distribution contains a shell script which is designed to transfer the datafiles to an fpc database. This script is called imtransfer and the configured $geltransfer command line for this script is :

imtransfer $projectpath $projectname $gelpath $gelnumber

2. configuring other transfer commands

There are other ways to use this facility which automatically calls a fully configurable program when a gel is finished. The Image results could be transferred to an inhouse Oracle or Acedb database. The configured geltransfer command may read from any of the datafiles in the $gelpath directory and then send them to the inhouse database. This command can be passed any of the parameters that are present in the info file of the gel.

Writing such a script will require some programming experience and knowledge of the target database system which will store the results.

It may be useful to include the complete directory path to the script-file to resolve ambiguities caused by different $PATH values in the shell-setup for different users.

The imtransfer script

After inspecting the target directory $FPCTOP_DIR the script creates directories /Image/ and /Gel/ in a directory called $projectname. The datafiles written by the gelfinalisation are then copied to their respective locations within the directory structure used by fpc. More more information check the content of the locally installed imtransfer script itself.

Last modified : November 1999 Image 3.10

* quick link - http://q.sanger.ac.uk/0p9m485s