AGCoL

Arizona Genomics
Computational Laboratory
Tucson, AZ

WebChrom Site Manual
WebAGCoL | User's Manual | FPC

CONTENTS

  1. PREREQUISITES
  2. HOW WebCHROM WORKS
  3. FILE FORMATS & CONFIG

PREREQUISITES

For WebChrom, the following software packages must be installed on your web server:

HOW WebCHROM WORKS   Back to top

The webchrom.pl script reads the FPC file, the chromosome file and references (see File Format). It writes the necessary files in <HTML_DIR_PATH>/WebAGCoL/<MAP_NAME>/WebChrom.

  • An index.html that displays the initial page of chromosomes.
  • For each chromosome or linkage group, the output directory contains the *.html files and *.png files.
  • A JavaScript/Jscript file named zmenu.js is also produced, containing code allowing the popup menus to work for each HTML file.
  • A sub-directory called DATA which contains "storeables" for the Search tool.
  • A 'tmp' directory in WebChrom folder of the project is created to which the Search tool writes temporary images generated for searches. (Note: These temperory image files are removed from the system by the script after 24 hours)
FILE FORMATS & CONFIG   Back to top

The following config variables are used: FPC_FILE, CHROMOSOME_FILE, REFERENCE_DIR.

All files in this section are put into the <HTML_DIR_PATH>/WebAGCoL/<MAP_NAME> directory by the setup.pl script, and can later be changed by the user (Note: the update.sh needs to be rerun after a change). This directory will be referred to as the MAP directory in the following discussion.

Chromosome File

The chromosome file is specified by the CHROMOSOME_FILE variable, and is copied to the config sub-directory of the MAP directory. This file contains the locations of the centromere for chromosomes and the sizes (in Mb) of the chromosomes. The file has two parts divided with the following specification:

<Chr or Lg> CENTROMERE_POS <3 digits.1 digit> [<3 digits.1 digit>]

and

<Chr or Lg> LENGTH <3 digits.1 digit>

For example: 


1  CENTROMERE_POS 73.5 73.5
2  CENTROMERE_POS  50 54.6

1  LENGTH 43.3
2  LENGTH 39.9
defines two chromosomes, both with centromeres. The centromere section is optional. The start and end coordinates of the centromere can be the same. The length is also optional; if absent, webchrom.pl will calculate a length based on the length of the contigs located on the chromosome.

Reference Files

The reference files are shared by both WebFPC and WebChrom, though WebChrom only uses the markers. See references for more information.

Email comments to vishal@genome.arizona.edu