Commits for hiram

v337_base to v338_preview (2016-08-15 to 2016-08-22) v338

2387766791f74cfaf8485356ea076687c7131e98 Mon Aug 15 11:34:47 2016 -0700

• do not remove the dot version from the gene name when verifying correspondence with pepTide name they all have version numbers now refs #17863
  
  • src/hg/utils/automation/doEnsGeneUpdate.pl - lines changed 1, context: html, text, full: html, text

21b9d6eee8b8cb0380c3349caa8af0fa90cd9174 Wed Aug 17 11:04:37 2016 -0700

• adding note about galGal5 parameters refs #17168
  
  • src/hg/makeDb/trackDb/mouse/mm10/vertebrateChainNet.html - lines changed 1, context: html, text, full: html, text

b6ce4b94768fc2c6587b94268d82a94842141181 Thu Aug 18 09:31:36 2016 -0700

• adding augustus gene track construction and clean up references to work hubs refs #13553
  
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 51, context: html, text, full: html, text
  • src/hg/utils/automation/doAugustus.pl - lines changed 25, context: html, text, full: html, text

dc8e0543646e48a1b8cb08c34a7b6c77c25bf9cf Thu Aug 18 10:13:33 2016 -0700

• adding augustus gene to trackDb and fixup errors refs #13553
  
  • src/hg/utils/automation/asmHubSimpleRepeat.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubWindowMasker.pl - lines changed 1, context: html, text, full: html, text

15792863307e32e65004b2db403c305c4fdd2532 Thu Aug 18 15:45:49 2016 -0700

• adding dropQ and dropT arguments to avoid garbage in NCBI gff3 files refs #13673
  
  • src/hg/utils/gff3ToPsl/gff3ToPsl.c - lines changed 28, context: html, text, full: html, text

f8c07173c3cc28fd490f767f24c511bca329bd89 Fri Aug 19 16:09:00 2016 -0700

• clean up and annotate generated processing shell files refs #13673
  
  • src/hg/utils/automation/doNcbiRefSeq.pl - lines changed 191, context: html, text, full: html, text

b69912c01829ac1b162eac9c43f801a049b07778 Fri Aug 19 18:14:17 2016 -0700

• eliminate bad records to allow continue refs #13673
  
  • src/hg/utils/automation/doNcbiRefSeq.pl - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/automation/gff3ToRefLink.pl - lines changed 3, context: html, text, full: html, text

1834d84f11c73a2ad3a3429c02941a5a3c6439b0 Mon Aug 22 10:05:41 2016 -0700

• v338 preview1 refs #17833
  
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text