File Changes for hiram

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

• src/hg/htdocs/inc/gbPageStartHardcoded.html
  • lines changed 1, 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/globalNavBar.inc
  • lines changed 1, 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/lib/genark.as
  • lines changed 11, 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.c
  • lines changed 243, 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.h
  • lines changed 86, 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.sql
  • lines changed 16, 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/makeDb/doc/asmHubs/hubIndex.pl
  • lines changed 2, 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/hubList.sh
  • lines changed 6, 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/master.run.list
  • lines changed 40, context: html, text, full: html, text
    e4558feb5286c7940fb287e05886b17be4970d30 Wed Apr 14 18:28:35 2021 -0700
    update to GenArk assemblies refs #23891
  • lines changed 4, 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/birdsAsmHub/birds.orderList.tsv
  • lines changed 6, 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/fishAsmHub/fish.orderList.tsv
  • lines changed 7, 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/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 31, 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/legacyAsmHub/legacy.orderList.tsv
  • lines changed 7, 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/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 5, 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/plantsAsmHub/plants.orderList.tsv
  • lines changed 57, 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/primatesAsmHub/primates.orderList.tsv
  • 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/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 8, 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/vgpAsmHub/vgp.alternate.orderList.tsv
  • lines changed 3, 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.legacy.orderList.tsv
  • lines changed 9, 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.primary.orderList.tsv
  • lines changed 18, 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.taxId.asmId.class.txt
  • lines changed 61, 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.trio.orderList.tsv
  • lines changed 17, 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/wuhCor1/vaccines.txt
  • lines changed 14, 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/trackDb/virus/wuhCor1/vaccines.html
  • lines changed 1, context: html, text, full: html, text
    5c9cf417c0e522b48807f6a21ee382c100e5e0fd Mon Apr 12 15:26:55 2021 -0700
    eliminate the Stanford name from the sequence refs #27312
  • 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/utils/automation/doAssemblyHub.pl
  • lines changed 8, context: html, text, full: html, text
    bf0cbaeb5efbf31609492be27319a3237996d522 Mon Apr 12 10:47:02 2021 -0700
    now construction dynamic blat indexes refs #26658
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 3, context: html, text, full: html, text
    b9ab779d8b7fdc353e57f056522f60c20e4e15a3 Mon Apr 12 10:48:27 2021 -0700
    correct recover from nestedRepeats problem no redmine