Commits for hiram

v421_base to v422_preview (2021-09-27 to 2021-10-04) v422

b973e754cafbb53bcb970d65e2c8e0915c6aa454 Mon Sep 27 14:57:29 2021 -0700

• convert hgPhyloPlace to earlyBotExit and remove dead botDelay code refs #28173
  • src/hg/hgPhyloPlace/hgPhyloPlace.c - lines changed 13, context: html, text, full: html, text
  • src/hg/inc/botDelay.h - lines changed 16, context: html, text, full: html, text
  • src/hg/lib/botDelay.c - lines changed 68, context: html, text, full: html, text

eabf4c3ee18afce4b36f7911b53364ad545ab33f Mon Sep 27 15:40:45 2021 -0700

• adding Trypanosoma cruzi GCF_000209065.1_ASM20906v1 to the invertebrates refs #28234
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkSymLinks.pl - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text

a29d4413f74fc087d4c99df4bd91a3b81eb4c350 Thu Sep 30 10:18:27 2021 -0700

• correct error message text no redmine
  • src/hg/utils/automation/asmHubGc5Percent.pl - lines changed 1, context: html, text, full: html, text

a1d34750a532bea424b58b6c27f9732b3c95ea73 Thu Sep 30 12:06:55 2021 -0700

• fix broken command syntax no redmine
  • src/hg/utils/automation/asmHubAssembly.pl - lines changed 2, context: html, text, full: html, text

060c692dfeda837e9fd0385123f75abbf378ceb7 Thu Sep 30 12:07:23 2021 -0700

• add download file for repeatMasker.out.gz results no redmine
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 9, context: html, text, full: html, text

a14381a65d94efd21600039ed9fb723fd8d5f51a Thu Sep 30 12:14:45 2021 -0700

• prevent divide by zero no redmine
  • src/hg/utils/automation/perlPara.pl - lines changed 2, context: html, text, full: html, text

7a27c931a0c34c30f39b810ae463d589627787a4 Thu Sep 30 13:48:26 2021 -0700

• correct arguments to doRecipBest when both genomes are assembly hubs no redmine
  • src/hg/utils/automation/pairLastz.sh - lines changed 24, context: html, text, full: html, text

8c3236684dfa12ba4f8841fab2dbe43127091148 Thu Sep 30 18:19:24 2021 -0700

• fixups to function correctly with both target and query are assembly hubs no redmine
  • src/hg/utils/automation/asmHubChainNet.pl - lines changed 201, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubChainNetTrackDb.sh - lines changed 16, context: html, text, full: html, text

f6a4d0f9523d06a6aa46e4ee4d96b37a4091d4a5 Thu Sep 30 18:20:31 2021 -0700

• correctly filter on chromSizes to eliminate out of range gene definitions no redmine
  • src/hg/utils/automation/doNcbiRefSeq.pl - lines changed 10, context: html, text, full: html, text

ac302e3245fa6e818c50dd4b8ac61338ae3d44a6 Sat Oct 2 00:35:17 2021 -0700

• catching up about 65 assemblies refs #23891
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 65, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 34, 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 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv - lines changed 1, context: html, text, full: html, text

37b85e32f377f44aca6f57162c38ac49cc70c678 Sat Oct 2 00:36:26 2021 -0700

• adding rmsk output to downloads and correctly getting assembly_report on downloads refs #23891
  • src/hg/makeDb/doc/asmHubs/mkSymLinks.pl - lines changed 3, context: html, text, full: html, text

b469ff8a02e3a013a11b3a2f930e51bca0dfbfb5 Sun Oct 3 21:54:36 2021 -0700

• add cgilib to the fetch script for the new tree organization refs #28240
  • src/userApps/fetchKentSource.sh - lines changed 1, context: html, text, full: html, text