Difference between revisions of "Developer documentation"
From WormBaseWiki
Jump to navigationJump to search| Line 1: | Line 1: | ||
This page contains information pertinent to developers of WormBase. | This page contains information pertinent to developers of WormBase. | ||
| − | = Development Strategy = | + | == Development Strategy == |
* [[Formal_development_strategy|Formal development strategy]] - ''An overview of the development process at WormBase'' | * [[Formal_development_strategy|Formal development strategy]] - ''An overview of the development process at WormBase'' | ||
| Line 7: | Line 7: | ||
*[[Coding standards|Coding standards]] | *[[Coding standards|Coding standards]] | ||
| − | = Developer Tools = | + | == Developer Tools == |
*Twitter: [http://twitter.com/wormbase-commits WormBase source commits]; [http://twitter.com/wormbase General announcements] | *Twitter: [http://twitter.com/wormbase-commits WormBase source commits]; [http://twitter.com/wormbase General announcements] | ||
| Line 13: | Line 13: | ||
*[http://www.wormbase.org/forums/index.php?board=326.0 WormBase Forum: Developer Forum] | *[http://www.wormbase.org/forums/index.php?board=326.0 WormBase Forum: Developer Forum] | ||
| − | == Source Code Repositories == | + | === Source Code Repositories === |
''We use the distributed source code management system Mercurial. Projects are hosted on [http://bitbucket.org BitBucket].'' | ''We use the distributed source code management system Mercurial. Projects are hosted on [http://bitbucket.org BitBucket].'' | ||
| Line 22: | Line 22: | ||
*[http://bitbucket.org/tharris/wormbase-admin WormBase-admin] - ''Administrative code (private)'' | *[http://bitbucket.org/tharris/wormbase-admin WormBase-admin] - ''Administrative code (private)'' | ||
| − | = Software platform = | + | == Software platform == |
*[[Application overview|Application overview]] - ''A quick tour through the software platform'' | *[[Application overview|Application overview]] - ''A quick tour through the software platform'' | ||
| Line 32: | Line 32: | ||
*[[Deployment|Deployment]] - ''How to deploy the web app for production use'' | *[[Deployment|Deployment]] - ''How to deploy the web app for production use'' | ||
| − | = Hardware platform = | + | == Hardware platform == |
*[[Logical structure|Logical structure]] | *[[Logical structure|Logical structure]] | ||
| Line 61: | Line 61: | ||
*[[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.'' | ||
| − | = 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 = | + | == Updates == |
*[[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'' | ||
*[[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'' | ||
| − | = Developer Meetings = | + | == Developer Meetings == |
[[2008.01-Toronto|14-18 January, 2008 - Toronto]] | [[2008.01-Toronto|14-18 January, 2008 - Toronto]] | ||
| − | = Presentations = | + | == Presentations == |
CSHL conference call slides | CSHL conference call slides | ||
| Line 82: | Line 82: | ||
| − | = Deprecated Documentation = | + | == Deprecated Documentation == |
''The good word gone bad. Cruft. Lint. Maybe useful but probably not.'' | ''The good word gone bad. Cruft. Lint. Maybe useful but probably not.'' | ||
Revision as of 00:31, 16 July 2009
This page contains information pertinent to developers of WormBase.
Contents
Development Strategy
- Formal development strategy - An overview of the development process at WormBase
- Developer notes - Best practices, conventions, etc
- Coding standards
Developer Tools
- Twitter: WormBase source commits; General announcements
- FriendFeed: WormBase FF 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)
- 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
Routine Administration Tasks
- Cronjobs
- Creating a Google Sitemap
- 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.
- Trac installation notes
- Trac Feature Tracker / Subversion repository
- Establishing the SVN repository - Setting up the subversion repository
