Commits for hiram

v413_base to v414_preview (2021-04-12 to 2021-04-19) v414

bf0cbaeb5efbf31609492be27319a3237996d522 Mon Apr 12 10:47:02 2021 -0700

• now construction dynamic blat indexes refs #26658
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 8, context: html, text, full: html, text

b9ab779d8b7fdc353e57f056522f60c20e4e15a3 Mon Apr 12 10:48:27 2021 -0700

• correct recover from nestedRepeats problem no redmine
  • src/hg/utils/automation/doRepeatMasker.pl - lines changed 3, context: html, text, full: html, text

7d0d819ed29f8a0501c3e8e99930b83ccdbf65e4 Mon Apr 12 14:01:50 2021 -0700

• genark table definition to relate GC accession to hub url refs #27285
  • src/hg/lib/genark.as - lines changed 11, context: html, text, full: html, text
  • src/hg/lib/genark.c - lines changed 243, context: html, text, full: html, text
  • src/hg/lib/genark.h - lines changed 86, context: html, text, full: html, text
  • src/hg/lib/genark.sql - lines changed 16, context: html, text, full: html, text

fd901859e155db29a2ed3ff2a71148aa3f5d0a69 Mon Apr 12 15:26:03 2021 -0700

• eliminate the Stanford name from the sequence refs #27312
  • src/hg/makeDb/doc/wuhCor1/vaccines.txt - lines changed 14, context: html, text, full: html, text

5c9cf417c0e522b48807f6a21ee382c100e5e0fd Mon Apr 12 15:26:55 2021 -0700

• eliminate the Stanford name from the sequence refs #27312
  • src/hg/makeDb/trackDb/virus/wuhCor1/vaccines.html - lines changed 1, context: html, text, full: html, text

92f881312be978ae7c9923c79a6a35f69559cced Mon Apr 12 16:46:17 2021 -0700

• eliminate the Stanford name from the sequence refs #27312
  • src/hg/makeDb/trackDb/virus/wuhCor1/vaccines.html - lines changed 1, context: html, text, full: html, text

e4558feb5286c7940fb287e05886b17be4970d30 Wed Apr 14 18:28:35 2021 -0700

• update to GenArk assemblies refs #23891
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 40, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 8, context: html, text, full: html, text

369a9bff649648dea01ee3f3b6ed3e027d71d28e Thu Apr 15 13:46:04 2021 -0700

• Genome Assembly Hubs becomes Genome Archive GenArk refs #23891
  • src/hg/htdocs/inc/gbPageStartHardcoded.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/inc/globalNavBar.inc - lines changed 1, context: html, text, full: html, text

c316bef9ca9fbaac700de97a076a46297102166f Thu Apr 15 13:55:04 2021 -0700

• now with title GenArk: UCSC Genome Archive and counting taxIds before and after update refs #23891
  • src/hg/makeDb/doc/asmHubs/hubIndex.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/hubList.sh - lines changed 6, context: html, text, full: html, text

8c7e2d4fcb982213c7bd2af77c67a0b8bff9c901 Fri Apr 16 07:23:15 2021 -0700

• catch up three VGP assemblies refs #23891
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 4, context: html, text, full: html, text

aab78e621acb6b1e45ae3ac32ab3c821247c8282 Mon Apr 19 09:07:24 2021 -0700

• catching up VGP assemblies refs #23891
  • src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.trio.orderList.tsv - lines changed 17, context: html, text, full: html, text

cc0f7e07de3a3ecadcb0b41ea2359b76cb63bf08 Mon Apr 19 09:58:25 2021 -0700

• up to date listings for VGP assemblies refs #23891
  • src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt - lines changed 61, context: html, text, full: html, text