Difference between revisions of "Developer documentation"
From WormBaseWiki
Jump to navigationJump to search| Line 5: | Line 5: | ||
*[http://www.wormbase.org/forums/index.php?board=326.0 WormBase Wiki: Developer Forum] | *[http://www.wormbase.org/forums/index.php?board=326.0 WormBase Wiki: Developer Forum] | ||
*[http://spreadsheets.google.com/ccc?key=pHvlNLMCZIv1KBoy8ZhbZXA&hl=en Migration matrix (GoogleDoc)] | *[http://spreadsheets.google.com/ccc?key=pHvlNLMCZIv1KBoy8ZhbZXA&hl=en Migration matrix (GoogleDoc)] | ||
| − | + | ||
= Useful Links = | = Useful Links = | ||
| Line 23: | Line 23: | ||
*[[Application overview|Application overview]] - ''A quick tour through the software platform'' | *[[Application overview|Application overview]] - ''A quick tour through the software platform'' | ||
| + | *[[Coding standards|Coding standards]] | ||
*[[Installing the Web Application|Installing the Web Application]] - ''Here's how to install the WormBase web application -- including Catalyst -- on your system'' | *[[Installing the Web Application|Installing the Web Application]] - ''Here's how to install the WormBase web application -- including Catalyst -- on your system'' | ||
*[[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'' |
*[[WormBase Development Environment|WormBase Development Environment]] - ''Building, Configuring, and Administering the WormBase development server'' | *[[WormBase Development Environment|WormBase Development Environment]] - ''Building, Configuring, and Administering the WormBase development server'' | ||
*[[Deployment|Deployment]] - ''How to deploy the web app for production use'' | *[[Deployment|Deployment]] - ''How to deploy the web app for production use'' | ||
| Line 48: | Line 49: | ||
*[[Crises Recovery Plan|Crises Recovery Plan]] - ''Everything breaks. Here's how to fix it.'' | *[[Crises Recovery Plan|Crises Recovery Plan]] - ''Everything breaks. Here's how to fix it.'' | ||
*[[Building WormMart|Building WormMart]] - ''How to convert a WormBase AceDB database into WormMart'' | *[[Building WormMart|Building WormMart]] - ''How to convert a WormBase AceDB database into WormMart'' | ||
| − | |||
| − | |||
| − | |||
== Load balancing and Failover == | == Load balancing and Failover == | ||
| Line 59: | Line 57: | ||
| − | |||
| − | |||
| − | |||
= OICR-specific documentation = | = OICR-specific documentation = | ||
| Line 82: | Line 77: | ||
Part 2: On Configuration ([http://www.wormbase.org/wiki/images/2008.02.13-on_configuration.key.tgz| key],[http://www.wormbase.org/wiki/images/2008.02.13-on_configuration.pdf| pdf]) -- ''Configuration basics (and freebies)'' | Part 2: On Configuration ([http://www.wormbase.org/wiki/images/2008.02.13-on_configuration.key.tgz| key],[http://www.wormbase.org/wiki/images/2008.02.13-on_configuration.pdf| pdf]) -- ''Configuration basics (and freebies)'' | ||
| + | |||
| + | |||
| + | == Deprecated Documentation == | ||
| + | |||
| + | ''The good word gone bad. Cruft. Lint. Maybe useful but probably not.'' | ||
| + | *[[Trac installation notes|Trac installation notes]] | ||
Revision as of 00:12, 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
- 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
OICR-specific documentation
- OICR-Configuring the development machine
- Building the WS200 frozen release
- 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.
