Commits for hiram

v415_base to v416_preview (2021-05-24 to 2021-06-01) v416

eaea1cfa2424b5d3754e0a50df60fa53c5074125 Mon May 24 10:24:49 2021 -0700

• better cleaning and do not load up the Ranges table refs #27546
  • src/hg/utils/automation/doCrispr.pl - lines changed 22, context: html, text, full: html, text

2eb7675b61bc79306e6ec54839140d2b40b31bf5 Mon May 24 12:19:29 2021 -0700

• canFam6 dog Tasha browser completed refs #27546
  • src/hg/makeDb/doc/canFam3.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/canFam4/initialBuild.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/canFam5/initialBuild.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/canFam6/initialBuild.txt - lines changed 92, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 74, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 68, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm39/lastzRuns.txt - lines changed 67, context: html, text, full: html, text

06f137f0b7d49def1d0690602cc10a6ad91eb083 Mon May 24 13:32:31 2021 -0700

• adding canFam6 chainNet definitions refs #27546
  • src/hg/makeDb/trackDb/human/chainNetPlacental.ra - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.chainNet.ra - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.mammal.ra - lines changed 60, context: html, text, full: html, text

91847e988b110028fedd701470e616f441f8fcd3 Mon May 24 14:05:11 2021 -0700

• adding in canFam6 chainNet RBest and SynNet definitions refs #27546
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.chainNet.ra - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.rbestNet.ra - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.syntenicNet.ra - lines changed 37, context: html, text, full: html, text

c7c0c4e70fbaac3739bca7a5d2c916a95c98155f Mon May 24 14:26:41 2021 -0700

• added version 104 definitions refs #27616
  • src/hg/utils/automation/EnsGeneAutomate.pm - lines changed 1697, context: html, text, full: html, text

5906ea1a00349cc4c2827103972f2f7728782823 Tue May 25 09:23:07 2021 -0700

• the omim tables are protected data refs #24208
  • src/hg/hubApi/apiUtils.c - lines changed 2, context: html, text, full: html, text

47f0e26225da2aa7f9d3f66d645c446a7ce70c5b Tue May 25 09:51:43 2021 -0700

• instead of a blanked elimination of omim table names, check for the noGenome trackDb setting refs #24208
  • src/hg/hubApi/apiUtils.c - lines changed 4, context: html, text, full: html, text

a30507e45e54053c6762a0daab762fc867cf94dc Tue May 25 14:00:07 2021 -0700

• correcting some broken species names refs #25555
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 7, context: html, text, full: html, text

ba856026204f578954c3cd7468c26d173e66d58f Fri May 28 11:37:58 2021 -0700

• correctly load RefSeqSelect table and add loading of RefSeqHgmd table for hg19 and hg38 refs #27575
  • src/hg/utils/automation/doNcbiRefSeq.pl - lines changed 36, context: html, text, full: html, text

1390c194b5568d35616a26e699e56a0858e5aad2 Fri May 28 13:43:15 2021 -0700

• otto update scripts runnin in /hive/data/outside/ncbi/genomes/ncbiRefSeq refs #27553
  • src/hg/makeDb/doc/ncbiRefSeq/ottoNcbiRefSeq.sh - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/ncbiRefSeq/prevHg19.sum - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/ncbiRefSeq/prevHg38.sum - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/ncbiRefSeq/prevMm10.sum - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/ncbiRefSeq/prevMm39.sum - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/ncbiRefSeq/runHg19.sh - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/ncbiRefSeq/runHg38.sh - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/ncbiRefSeq/runMm10.sh - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/ncbiRefSeq/runMm39.sh - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/ncbiRefSeq/runUcscDb.sh - lines changed 43, context: html, text, full: html, text