Difference between revisions of "Developer documentation"
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This page contains information pertinent to developers of WormBase. | This page contains information pertinent to developers of WormBase. | ||
| − | = | + | = Developer Tools = |
*[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:// | + | *[http://twitter.com/wormbase-commits WormBase-commits on Twitter] |
| − | + | *[http://friendfeed.com/wormbase WormBase FriendFeed room] | |
| − | + | *[http://www.wormbase.org/forums/index.php?board=326.0 WormBase Forum: Developer Forum] | |
| − | |||
== Source Code Repositories == | == Source Code Repositories == | ||
| Line 21: | Line 20: | ||
*[[Application overview|Application overview]] - ''A quick tour through the software platform'' | *[[Application overview|Application overview]] - ''A quick tour through the software platform'' | ||
| + | *[http://spreadsheets.google.com/ccc?key=pHvlNLMCZIv1KBoy8ZhbZXA&hl=en Migration matrix (GoogleDoc)] | ||
*[[Coding standards|Coding standards]] | *[[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'' | ||
| Line 41: | Line 41: | ||
*[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'' | *[[WormBase Development Environment|WormBase Development Environment]] - ''Building, Configuring, and Administering the WormBase development server'' | ||
| − | |||
| − | |||
*[[Managing GBrowse]] - ''Quick HowTo for managing GBrowse in development and production environments'' | *[[Managing GBrowse]] - ''Quick HowTo for managing GBrowse in development and production environments'' | ||
| − | + | *[[Log file management and analysis|Log file management and analysis]] - ''rotating and analyzing logs'' | |
| − | *[[ | ||
| − | |||
| − | |||
== Load balancing and Failover == | == Load balancing and Failover == | ||
| − | |||
*[[Building Squid|Building Squid]] - ''How to build and install Squid'' | *[[Building Squid|Building Squid]] - ''How to build and install Squid'' | ||
*[[Configuring Squid|Configuring Squid]] - ''basic squid configuration at WormBase'' | *[[Configuring Squid|Configuring Squid]] - ''basic squid configuration at WormBase'' | ||
| − | *[[ | + | |
| + | == Monitoring and Crises Management == | ||
| + | *[[Monitoring services and servers|Monitoring services and servers]] | ||
| + | *[[Crises Recovery Plan|Crises Recovery Plan]] - ''Everything breaks. Here's how to fix it.'' | ||
= OICR-specific documentation = | = OICR-specific documentation = | ||
*[[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'' | ||
*[[Migrating frozen releases to OICR]] | *[[Migrating frozen releases to OICR]] | ||
| + | |||
| + | = Updates = | ||
| + | *[[Updating The Development Server]] - ''Updating the development server with a new release of the database'' | ||
| + | *[[Building WormMart|Building WormMart]] - ''How to convert a WormBase AceDB database into WormMart'' | ||
= Developer Meetings = | = Developer Meetings = | ||
Revision as of 00:23, 16 July 2009
This page contains information pertinent to developers of WormBase.
Contents
Developer Tools
- WormBase Wiki: Developer Forum
- WormBase-commits on Twitter
- WormBase FriendFeed room
- WormBase Forum: Developer Forum
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
- Migration matrix (GoogleDoc)
- 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
- Managing GBrowse - Quick HowTo for managing GBrowse in development and production environments
- Log file management and analysis - rotating and analyzing logs
Load balancing and Failover
- Building Squid - How to build and install Squid
- Configuring Squid - basic squid configuration at WormBase
Monitoring and Crises Management
- Monitoring services and servers
- Crises Recovery Plan - Everything breaks. Here's how to fix it.
OICR-specific documentation
- WormBase Development Environment - Building, Configuring, and Administering the WormBase development server
- Migrating frozen releases to OICR
Updates
- Updating The Development Server - Updating the development server with a new release of the database
- Building WormMart - How to convert a WormBase AceDB database into WormMart
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.
