2010.05 OICR WebDev Meeting

Meeting summary

BioMart

• Abby: built WS205, migrated to new biomart machine

TODO

• Abby: might be some configuration problems with Apache
• TH: setting up as subdomain, virtual host

Development Update Pipeline

• Norie: added support for mirroring pre-prepared GFF mysql databases fom Sanger

TODO

• Continue update to WS214
• GFF MySQL code to be tested with WS215

modENCODE

• Xiaoqi: migrated current modENCODE data to production
• Emailed dev list
• Added caveat

TODO

• Need to copy over configuration stanzas to production configuration files
  • GBrowse-1.70
  • GBrowse-2.03

GBrowse

• Debugged various plugin issues
• SequenceDumper.pm and FastaDumper.pm issues

TODO

• add initial landmark config
• set up GBrowse 1.x @ OICR and update proxy
• XQ: Ensure feature parity between GB1/GB2
• Resolve preservation of track selection prefs problem
• TH: Karyotype hosting?
• resolve keyword searching issue (ie unc-9)
• Sanger: nucleosome data

Rearchitecture

Database Connectivity

• Xiaoqi: converting from lock based method to one checking status
• Xiaoqi: code done next week or so.

API

• Standardized data structure
• Expanded class coverage
• Norie working on additional classes

TODO

• TH: prioritize order in which classes/pages should be converted.

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QA/QC meetings

Visit goals

• Benchmarks
• Tests
• Documentation
• Sanger Databases
• Issue Tracker issues
• OICR aceserver