Difference between revisions of "WebDev 2009.06.16-Agenda and Minutes"

From WormBaseWiki
Jump to navigationJump to search
 
(3 intermediate revisions by the same user not shown)
Line 8: Line 8:
 
* [[Migrating_frozen_releases_to_OICR]]
 
* [[Migrating_frozen_releases_to_OICR]]
  
Moved to: mod_perl2/apache2, GBrowse2
+
In migrating, reconciled four long-standing back burner issues:
 
 
  
 
* localized libraries
 
* localized libraries
Line 16: Line 15:
 
* GBrowse 2
 
* GBrowse 2
  
LS:  
+
GBrowse2:
 +
* LS: Check to make sure using preforked and not multi-threaded Apache.
 +
* TH: finishing up migration of configuration files
  
 +
* LS: Include feature from common elements
 +
** #include path/*  // for example
  
 
Aggregator issues
 
Aggregator issues
  *  Aggregator has to be associated with the database  
+
* Custom wormbase gene aggregator not working
 +
* LS: Bio::DB::SeqFeature?
 +
* TH: Nope, Bio::DB::GFF
 +
*  Aggregator has to be associated with the database conf, not GBrowse.conf
  
 
gbrowse_img:
 
 
tmpimages
 
tmpimages
  * in the main gbrowse.conf
+
* TH: available in GB1, used primarily for resolving backend machines generating gbrowse_img pics
  * apache config stanza
+
* LS: now handled by apache config stanza
   * mapping from temporary URL space to physical space; adjust to do spacing
+
   ** mapping from temporary URL space to physical space; adjust to do spacing
  
 
== 3. modENCODE Update (Marc, Peter, Zheng; 30 minutes) ==
 
== 3. modENCODE Update (Marc, Peter, Zheng; 30 minutes) ==
 +
 +
Peter:
 +
* Duplicated tracks - regular expression not capturing pattern appropriately
 +
* Nicole working with Waterston on additional data sets
 +
 +
 +
Marc:
 +
 +
Zheng:
 +
WormMart and modENCODE BioMart
 +
 +
BioMart will have central port that will point to development server
 +
 +
* TH: Where will the database live?  Do we need to host?
 +
* '''ZZ: Will discuss with Arek'''
  
 
== 4. Open Table ==
 
== 4. Open Table ==
 +
 +
NO CONFERENCE CALL NEXT WEEK DUE TO THE INTERNATIONAL WORM MEETING

Latest revision as of 09:38, 1 July 2009

1. Administration (Todd, 5 minutes)

2. Describe OICR migration progress (Todd, 10 minutes)

See:

In migrating, reconciled four long-standing back burner issues:

  • localized libraries
  • mod_perl2
  • apache2
  • GBrowse 2

GBrowse2:

  • LS: Check to make sure using preforked and not multi-threaded Apache.
  • TH: finishing up migration of configuration files
  • LS: Include feature from common elements
    • #include path/* // for example

Aggregator issues

  • Custom wormbase gene aggregator not working
  • LS: Bio::DB::SeqFeature?
  • TH: Nope, Bio::DB::GFF
  • Aggregator has to be associated with the database conf, not GBrowse.conf

tmpimages

  • TH: available in GB1, used primarily for resolving backend machines generating gbrowse_img pics
  • LS: now handled by apache config stanza
 ** mapping from temporary URL space to physical space; adjust to do spacing

3. modENCODE Update (Marc, Peter, Zheng; 30 minutes)

Peter:

  • Duplicated tracks - regular expression not capturing pattern appropriately
  • Nicole working with Waterston on additional data sets


Marc:

Zheng: WormMart and modENCODE BioMart

BioMart will have central port that will point to development server

  • TH: Where will the database live? Do we need to host?
  • ZZ: Will discuss with Arek

4. Open Table

NO CONFERENCE CALL NEXT WEEK DUE TO THE INTERNATIONAL WORM MEETING