Use of Freedberg Script

Overview
This script (standardly labeled freedberg.pl) is being used to gage the significance of a Biology faculty member's findings regarding the Tetrahymena genome. As the project of actually using the script on the cluster is likely to be passed from person to person (as it has been already), it seems sage to write some basic directions for future use.

Using the Script
The script is actually quite simple. All required parameters are provided to it via a file (unfortunately, named simply 'file' at the moment). This file provides a way for instances of freedberg.pl to find their running parameters (a single integer variable) based on the cluster node they are currently running on.

To run the script, simply submit it to SGN by the usual method and make certain 'file' is in the same directory as the script.

Parsing Output
Output will be printed to standard output (and therefore the file SGE stores such output to) in a three line format like this: h-001 20071009_1055 h-001 The tally of total ORFs: 184 h-001 The tally of ORFs 0.8 the size of the original: 436

The first line tells you the specific designation of the node returning the output. The next two lines each end with an integer. These pairs of integers (coupled with the parameter under-which they were obtained) are the data you're looking for.

Involved Files
Here is a link to the code of freedberg.pl v1.2 (at the moment it should be accessible only to people enrolled in the capstone class): http://www.cs.stolaf.edu/projects/beowulf/local/cap.F07/

freedberg pl code (this secondary link will be removed once the primary one starts working)

Here is an example of the 'file' datafile (the one being used on Helios as of Oct 07): h-001 510 h-002 510 h-003 510 h-004 510 h-005 540 h-006 540 h-007 540 h-008 540 h-009 570 h-010 570 h-011 570 h-012 570 h-013 600 h-014 600 h-015 600 h-016 600 h-017 600