Commits for hiram

v411_preview2 to v411_base (2021-02-22 to 2021-03-01) v411

81c8061cf668e009c5222909840074a8ae57166e Mon Feb 22 12:22:11 2021 -0800

• adding xenTro10 to the browser refs #24693
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenTro10/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenTro10/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenTro10/gold.html - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenTro10/trackDb.ra - lines changed 8, context: html, text, full: html, text

2b386db2505e864fef06874aa394578431abfefc Mon Feb 22 13:26:52 2021 -0800

• adding gold table assembly track search rule refs #24693
  • src/hg/makeDb/trackDb/xenTro/xenTro10/trackDb.ra - lines changed 5, context: html, text, full: html, text

00bf66b33a1aaf94662da3947525b151a3fb9fd8 Mon Feb 22 13:32:31 2021 -0800

• initial db done running up RM and TRF refs #24693
  • src/hg/makeDb/doc/xenTro10/initialBuild.txt - lines changed 1449, context: html, text, full: html, text

98d802668211742e7f43a7563bb91f7830f7d54e Mon Feb 22 22:03:30 2021 -0800

• add refSeqComposite refs #24693
  • src/hg/makeDb/trackDb/xenTro/xenTro10/trackDb.ra - lines changed 2, context: html, text, full: html, text

a001152197ed70e4192a3ecf1db4e9efc4e34ce4 Mon Feb 22 22:08:40 2021 -0800

• adding rules for xenTro10 refs #24693
  • src/hg/makeDb/schema/all.joiner - lines changed 9, context: html, text, full: html, text

96eadc884d440309b56203fcbdf7b2bfa9ab1a7c Wed Feb 24 13:38:18 2021 -0800

• initial set non-unique common names refs #27072
  • src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv - lines changed 355, context: html, text, full: html, text
  • src/hg/makeDb/doc/fungiAsmHub/hub.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/fungiAsmHub/makefile - lines changed 26, context: html, text, full: html, text

51d63f5c477d789b0cc6fc94ec9fd6387e7d99dc Wed Feb 24 13:39:08 2021 -0800

• and with unique common names refs #27072
  • src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv - lines changed 345, context: html, text, full: html, text

d08acbc51365288f679e20b71ebe3a51da8c80e1 Wed Feb 24 14:30:47 2021 -0800

• correctly process non-nuclear unlocalized sequence refs #27072
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 3, context: html, text, full: html, text

9a4fce5401a6b405d65f2c05e1e3424d6cf6892c Thu Feb 25 09:49:24 2021 -0800

• adding fungi run list refs #27072
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 355, context: html, text, full: html, text

08cee46a18fa261f2af2d711d666b4ec3dbfd855 Thu Feb 25 11:39:12 2021 -0800

• mRatBN7.2 became a GCF release refs #23891
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 1, context: html, text, full: html, text

ebf2d6bb1cefc1fdf1dec9548002bd0b7600340d Thu Feb 25 11:40:21 2021 -0800

• catching up a few assemblies refs #23891
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 6, context: html, text, full: html, text

0736936b377d71bc19c0aa3b4311bc3872f76d54 Thu Feb 25 11:40:51 2021 -0800

• catching up a few assemblies refs #23891
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 1, context: html, text, full: html, text

b4dc9b3c2392cdc04e21b7d7e0cbd4f0f44c291c Thu Feb 25 11:41:18 2021 -0800

• catching up a few assemblies refs #23891
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 2, context: html, text, full: html, text

65e66bfd2166612d6aa23ab8741bea63e76417e7 Thu Feb 25 11:42:16 2021 -0800

• catching up a few assemblies refs #26765
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 9, context: html, text, full: html, text

6964f094f71a69fa083dbe3a6d88dc84f60b0855 Thu Feb 25 11:44:28 2021 -0800

• expanded link to other hubs table refs #23891
  • src/hg/makeDb/doc/asmHubs/commonHtml.pm - lines changed 49, context: html, text, full: html, text

f0874c9f03bf0f37bf7365813dce7e83d549f6d5 Thu Feb 25 12:38:39 2021 -0800

• adding the purple sea urchin refs #27032
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text

41946fe619f5dd532050be9fdbf6a1af1ebcd198 Fri Feb 26 11:52:30 2021 -0800

• turning on refSeq all instead of just curated refs #27067
  • src/hg/makeDb/trackDb/marmoset/calJac4/customRefSeqComposite.ra - lines changed 195, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac4/trackDb.ra - lines changed 1, context: html, text, full: html, text

b5ba1cd9de8155e0d9110426bb5e137b78f708d6 Sat Feb 27 17:50:21 2021 -0800

• rought notes on constructing the 241-way track from the cactus hal file no redmine
  • src/hg/makeDb/doc/hg38/cactus241way.txt - lines changed 924, context: html, text, full: html, text

3a98f0a9c8b6e1771f09cd38d2cf68a7a691c860 Mon Mar 1 08:22:44 2021 -0800

• need to use the appropriate chrom name column when getting full table refs #25840
  • src/hg/hubApi/getData.c - lines changed 2, context: html, text, full: html, text