Developer documentation

This page contains information pertinent to developers of WormBase.

Getting started

• WormBase Wiki: Developer Forum
• Migration matrix (GoogleDoc)
• HOWTO migrate a CGI - quick overview of how to migrate an existing CGI into a Model, Controller, and View. Sparse

Useful Links

Source Code Repositories

We use the distributed source code management system Mercurial. Projects are hosted on BitBucket.

How-To create, check out, and manage our repositories

• WormBase - The WormBase web application (public)
• WormBase-admin - Administrative code (private)

• Trac Feature Tracker / Subversion repository

Software platform

• Application overview - A quick tour through the software platform
• Installing the Web Application - Here's how to install the WormBase web application -- including Catalyst -- on your system
• Common Model elements - reference list of common model elements handled generically
• Coding standards
• WormBase Development Environment - Building, Configuring, and Administering the WormBase development server
• Deployment - How to deploy the web app for production use

Hardware platform

• Logical structure
• Physical structure
• MySQL database replication - Mirroring mysql databases across production nodes
• Performance optimization - Memory, Disk, and Network I/O troubleshooting
• Hardware catalog - A complete accounting of WormBase compute resources
• Base node configuration - CentOS5 - Configuring a WormBase node from scratch (CentOS 5)
• Building a production node - Configuring a new production node

Administration

• WormBase-admin (mercurial; Bitbucket) - The WormBase administration code repository (private)
• Updating The Development Server - Updating the development server with a new release of the database
• Managing GBrowse - Quick HowTo for managing GBrowse in development and production environments

• Monitoring services and servers
• Crises Recovery Plan - Everything breaks. Here's how to fix it.
• Building WormMart - How to convert a WormBase AceDB database into WormMart

Load balancing and Failover

• Building Squid - How to build and install Squid
• Configuring Squid - basic squid configuration at WormBase
• Log file management and analysis - rotating and analyzing logs

Deprecated Documentation

The good word gone bad. Cruft. Lint. Maybe useful but probably not.

• Trac installation notes

OICR-specific documentation

• OICR-Configuring the development machine
• Building the WS200 frozen release
• Migrating frozen releases to OICR

Developer Meetings

14-18 January, 2008 - Toronto

Presentations

CSHL conference call slides

Part 1: Introduction (key, pdf)-- Catalyst, the reimplementation strategy, and roadmap

Part 2: On Configuration (key,pdf) -- Configuration basics (and freebies)