Difference between revisions of "Developer documentation"
From WormBaseWiki
Jump to navigationJump to search| Line 27: | Line 27: | ||
*[[Common Model elements|Common Model elements]] - ''reference list of common model elements handled generically'' | *[[Common Model elements|Common Model elements]] - ''reference list of common model elements handled generically'' | ||
*[[HOWTO migrate a CGI|HOWTO migrate a CGI]] - ''quick overview of how to migrate an existing CGI into a Model, Controller, and View. Sparse'' | *[[HOWTO migrate a CGI|HOWTO migrate a CGI]] - ''quick overview of how to migrate an existing CGI into a Model, Controller, and View. Sparse'' | ||
| − | |||
*[[Deployment|Deployment]] - ''How to deploy the web app for production use'' | *[[Deployment|Deployment]] - ''How to deploy the web app for production use'' | ||
| Line 43: | Line 42: | ||
*[http://bitbucket.org/tharris/wormbase-admin WormBase-admin (mercurial; Bitbucket)] - ''The WormBase administration code repository (private)'' | *[http://bitbucket.org/tharris/wormbase-admin WormBase-admin (mercurial; Bitbucket)] - ''The WormBase administration code repository (private)'' | ||
| + | *[[WormBase Development Environment|WormBase Development Environment]] - ''Building, Configuring, and Administering the WormBase development server'' | ||
| + | |||
*[[Updating The Development Server]] - ''Updating the development server with a new release of the database'' | *[[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'' | *[[Managing GBrowse]] - ''Quick HowTo for managing GBrowse in development and production environments'' | ||
| Line 55: | Line 56: | ||
*[[Configuring Squid|Configuring Squid]] - ''basic squid configuration at WormBase'' | *[[Configuring Squid|Configuring Squid]] - ''basic squid configuration at WormBase'' | ||
*[[Log file management and analysis|Log file management and analysis]] - ''rotating and analyzing logs'' | *[[Log file management and analysis|Log file management and analysis]] - ''rotating and analyzing logs'' | ||
| − | |||
| − | |||
| − | |||
= OICR-specific documentation = | = OICR-specific documentation = | ||
Revision as of 00:15, 16 July 2009
This page contains information pertinent to developers of WormBase.
Contents
Getting started
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)
Software platform
- Application overview - A quick tour through the software platform
- Coding standards
- 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
- HOWTO migrate a CGI - quick overview of how to migrate an existing CGI into a Model, Controller, and View. Sparse
- 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)
- WormBase Development Environment - Building, Configuring, and Administering the WormBase development server
- 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
OICR-specific documentation
- WormBase Development Environment - Building, Configuring, and Administering the WormBase development server
- Migrating frozen releases to OICR
Developer Meetings
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)
Deprecated Documentation
The good word gone bad. Cruft. Lint. Maybe useful but probably not.
