galt: changes by commit

branch to review (2009-05-12 to 2009-05-19) v206

• Added aplCal1 to DBS.
  • src/hg/makeDb/trackDb/makefile 1.267 - lines changed: 1, context: html, text, full: html, text
• Initial Aplysia californica
  • src/hg/makeDb/doc/aplCal1.txt 1.3 - lines changed: 50, context: html, text, full: html, text
  • src/hg/makeDb/doc/aplCal1.txt 1.2 - lines changed: 16, context: html, text, full: html, text
  • src/hg/makeDb/doc/aplCal1.txt 1.1 - lines changed: 52, context: html, text, full: html, text
• refactored to all udcFileCacheFiles to operate without requiring the url to be actually opened
  • src/inc/udc.h 1.10 - lines changed: 3, context: html, text, full: html, text
  • src/lib/udc.c 1.17 - lines changed: 71, context: html, text, full: html, text
• add touching of udc files in cache and reporting of names for the do-not-kill-list with verbose=4
  • src/hg/lib/customFactory.c 1.97 - lines changed: 26, context: html, text, full: html, text
• tweak to handle udcCache location and process dataUrl setting to touch files in cache and report them for the do-not-kill list
  • src/hg/utils/refreshNamedSessionCustomTracks/makeExclusionList.pl 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c 1.9 - lines changed: 3, context: html, text, full: html, text
• handling udc cache files touching
  • src/hg/utils/refreshNamedSessionCustomTracks/refreshSledgeHammer.pl 1.3 - lines changed: 1, context: html, text, full: html, text
• Try to deal with lost Mysql connection after long waits for validate or load
  • src/hg/encode/hgEncodeSubmit/config/environment.rb.sample 1.3 - lines changed: 6, context: html, text, full: html, text
  • src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb 1.13 - lines changed: 4, context: html, text, full: html, text
• fixed typo
  • src/hg/utils/refreshNamedSessionCustomTracks/makeExclusionList.pl 1.6 - lines changed: 1, context: html, text, full: html, text
• remove what does not work
  • src/hg/encode/hgEncodeSubmit/config/environment.rb.sample 1.4 - lines changed: 1, context: html, text, full: html, text