Commits for hiram

v320_base to v321_preview (2015-08-03 to 2015-08-21) v321

• more correct parsing of FTP site listing refs #15796
  
  • src/hg/utils/automation/findEnsFtpNames.sh - lines changed 3, context: html, text, full: html, text
• now using -includeVersion for gtfToGenePred and subsequent correct name matching from gene to protein refs #15796
  
  • src/hg/utils/automation/doEnsGeneUpdate.pl - lines changed 4, context: html, text, full: html, text
• actually on chlSab2 instead of chlSab1 refs #15796
  
  • src/hg/utils/automation/EnsGeneAutomate.pm - lines changed 3, context: html, text, full: html, text
• actually dm6 in v81 instead of dm3 refs #15796
  
  • src/hg/utils/automation/EnsGeneAutomate.pm - lines changed 3, context: html, text, full: html, text
• ensGene names can be up to 21 characters refs #15796
  
  • src/hg/lib/ensGtp.sql - lines changed 2, context: html, text, full: html, text
• ensGene names can be up to 21 characters refs #15796
  
  • src/hg/lib/ensGtp.sql - lines changed 2, context: html, text, full: html, text
• updated email addresses to proper at soe.ucsc.edu refs #15731
  
  • src/utils/qa/weeklybld/cherryPickCommits.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/weeklybld/doNewBranch.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/weeklybld/doSearchRobot.csh - lines changed 2, context: html, text, full: html, text
  • src/utils/qa/weeklybld/moveBranchTag.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/weeklybld/patchBranch.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/weeklybld/revertCommits.csh - lines changed 1, context: html, text, full: html, text
• adding ci3 to match Ensembl releases refs #15796
  
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirt/ci3/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirt/ci3/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirt/ci3/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirt/ci3/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/automation/makeGenomeDb.pl - lines changed 1, context: html, text, full: html, text
• adding ci3 to correspond with Ensembl v81 release refs #15796
  
  • src/hg/makeDb/doc/ci3/initialBuild.txt - lines changed 648, context: html, text, full: html, text
  • src/hg/makeDb/doc/ci3/ucscCompositeAgp.pl - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/doc/ci3/unplaced.pl - lines changed 48, context: html, text, full: html, text
• adding search rule for gold table refs #15796
  
  • src/hg/makeDb/trackDb/squirt/ci3/trackDb.ra - lines changed 5, context: html, text, full: html, text
• v321 preview1 refs #15836
  
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text