Commits for hiram

v444_preview2 to v444_base (2023-02-13 to 2023-02-20) v444

b7d1b1b10c2fa9a037b3104bb2540e02da60e3ec Mon Feb 13 10:39:47 2023 -0800

• replace the obsolete chromAliasToTxt.pl with the aliasTabToText.pl equivalent no redmine
  • src/hg/utils/automation/aliasTabToText.pl - lines changed 69, context: html, text, full: html, text
  • src/hg/utils/automation/chromAliasToTxt.pl - lines changed 5, context: html, text, full: html, text

9ea6efeaf7d92fa6d49865aa8f2bcfa3e72272a9 Mon Feb 13 10:57:42 2023 -0800

• document the chromAlias construction for both chromAlias table and download files no redmine
  • src/hg/makeDb/doc/vicPac2.txt - lines changed 111, context: html, text, full: html, text

98874f1656202cd5781466a5d9b25f47da1f104d Mon Feb 13 16:03:53 2023 -0800

• a bit closer to correct NCBI links, not perfect, but better than it was no redmine
  • src/hg/hgTracks/extTools.c - lines changed 6, context: html, text, full: html, text
  • src/hg/hgTracks/menu.c - lines changed 14, context: html, text, full: html, text
  • src/hg/inc/asmEquivalent.h - lines changed 3, context: html, text, full: html, text
  • src/hg/inc/chromAlias.h - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/asmEquivalent.c - lines changed 10, context: html, text, full: html, text
  • src/hg/lib/chromAlias.c - lines changed 53, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 3, context: html, text, full: html, text

bfb9aa1b3a8a17c3100f6e7570bb55dd4b00d46c Tue Feb 14 08:18:45 2023 -0800

• checking in crispor update no redmine
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 197, context: html, text, full: html, text

830d7ce0370d22ff771e703d3ea2d2c4680b20cd Tue Feb 14 08:30:28 2023 -0800

• adding Asian tiger no redmine
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 1, context: html, text, full: html, text

85ea918488f0ea187d32633718810982b91ece09 Tue Feb 14 09:08:58 2023 -0800

• mosquito is not a primate no redmine
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 1, context: html, text, full: html, text

ec301d2ed3e444a70ac83f03586daf2db375288d Wed Feb 15 10:07:50 2023 -0800

• change grcIncident to 6 AM instead of 9 AM to avoid mysterious interference no redmine
  • src/hg/utils/otto/otto.crontab - lines changed 1, context: html, text, full: html, text

8568eb14b474e031f19a108acf516646fa05ba0d Wed Feb 15 10:10:52 2023 -0800

• eliminate a bunch of duplicates that were mistakenly checked in no redmine
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 85, context: html, text, full: html, text

3cdd218974321e097486b7ac68e147e9785612b2 Wed Feb 15 10:16:38 2023 -0800

• something broke down with the clade classification system fixed bogus duplicate entries no redmine
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 11, context: html, text, full: html, text

b7dd2ec4d968aa3adb8dc2abf8e50e1b4d1e5b32 Wed Feb 15 14:28:25 2023 -0800

• updating to add 3 viral sequences refs #29545
  • src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv - lines changed 3, context: html, text, full: html, text

a9e5c878cb63422a19c9ad6564d1588c5df10c9f Wed Feb 15 16:56:29 2023 -0800

• adding a nematode per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text

23d4ca1bff614e40ff402f54fca6771bddcfc351 Wed Feb 15 17:00:47 2023 -0800

• adding a nematode O.tipulae CEW1 2020 per user request refs #29545
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text

404562a0949bf43b853017fa20a6fc70d22d4ccc Thu Feb 16 11:43:56 2023 -0800

• update to GenArk hubs per user requests refs #29545
  • src/hg/makeDb/doc/asmHubs/asmHubs.mk - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/commonNames.pl - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv - lines changed 40, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 35, context: html, text, full: html, text

58839314d83dd1b8a70c0d41969e9e9eb67dc53b Thu Feb 16 14:54:38 2023 -0800

• adding bacteria sequences per user request refs #29545
  • src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 31, context: html, text, full: html, text

1a2aa31bfa14f809ee4093cea7b436e331b86ff4 Thu Feb 16 14:56:34 2023 -0800

• improved common names for fungi and bacteria an lower limits for valid number of tracks in bacteria and plants refs #29545
  • src/hg/makeDb/doc/asmHubs/commonNames.pl - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh - lines changed 2, context: html, text, full: html, text

403c5b11948650301cfd70fbaa521c08c3723169 Fri Feb 17 11:48:49 2023 -0800

• catch up to CCGP assemblies no redmine
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 2, context: html, text, full: html, text

e710ecdfe8a38cd878fbb93b4b53df847c0d168b Fri Feb 17 12:11:44 2023 -0800

• catching up to CCGP list of genomes no redmine
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 2, context: html, text, full: html, text

2e620bc3f85609612abd64cf5ef4cb8edd3e3dbf Fri Feb 17 12:13:28 2023 -0800

• catching up to CCGP list of genomes no redmine
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 3, context: html, text, full: html, text

8a972a814894c3c825fd8d7c4019d288dda40d32 Fri Feb 17 12:13:44 2023 -0800

• catching up to CCGP list of genomes no redmine
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 2, context: html, text, full: html, text

aff749c5723ebbde6bb1fa33546c06fae1dec455 Fri Feb 17 12:19:20 2023 -0800

• catching up to CCGP list of genomes no redmine
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 2, context: html, text, full: html, text

c7d20855bc1689ff0d6f85d113c2e735d4f5329c Fri Feb 17 13:00:13 2023 -0800

• clarify versions of the Yangtze porpoise no redmine
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 1, context: html, text, full: html, text

4865125e312f383396ea8d7080dbd1fefdcf6f9e Fri Feb 17 13:00:56 2023 -0800

• catch up an older version of the porpoise which is in CCGP no redmine
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 1, context: html, text, full: html, text

06b372f6628c2c35eebb105d5f5d6262b23e6d5c Sun Feb 19 15:36:21 2023 -0800

• some improvements after running through every single RefSeq assembly no redmine
  • src/hg/makeDb/doc/asmHubs/commonNames.pl - lines changed 23, context: html, text, full: html, text