Chado Tables to Wiki

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Revision as of 04:05, 15 April 2007 by Bosborne (Talk | contribs)

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Description

This page shows you how to create the Chado table documentation seen on pages like Chado Tables and Chado Organism Module.

Instructions

The postgresql_autodoc script uses template files to create HTML documentation of Postgres schemas. To create table documentation for this Wiki you will use one template file to create the documentation for the entire Chado schema (Chado Tables, where all links are internal) and another template to create table documentation for a module (e.g. Chado Organism Module, where all links go to Chado Tables page). A simple Perl script converts the HTML to Wiki text.

  • Install postgresql_autodoc (http://www.rbt.ca/autodoc/)
  • Save this text as html.tmpl if you want to create table documentation for the entire schema
  • Save this text as html.tmpl if you want to create table documentation for a single module
  • Run the postgresql_autodoc script in the same directory as the html.tmpl file. The command will be something like this:
  >postgresql_autodoc -f chado -u user -d chado --password=passwd -l . 
  • This should create an HTML file called chado.html
  • Run this Perl script to convert the HTML to Wiki text
  • If you're creating table documentation for the entire schema the command will look something like this:
  >print-wiki-tables.pl -all > allmodules.wiki
  • If you're creating table documentation for a module the command will look something like this:
 >print-wiki-tables.pl -m cv > cv.wiki