Commits for hiram

v485_base to v486_preview (2025-07-21 to 2025-07-28) v486

cb718a9f9f9d2c9d43a92a618da91be0de85ed3d Mon Jul 21 16:32:16 2025 -0700

• document the findGenome endpoint and reveal the /list/genarkGenomes endpoing function refs #35468
  • src/hg/htdocs/goldenPath/help/api.html - lines changed 32, context: html, text, full: html, text

6a00887793c65562b2d7ed2f5abe5feb9dd3a7e3 Mon Jul 21 17:35:20 2025 -0700

• adding one per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 3, context: html, text, full: html, text

bd7ad41f40025e2d8d08ea6a001507b935a8ff5d Mon Jul 21 17:39:50 2025 -0700

• adding archaea as a new group refs #29545
  • src/hg/makeDb/doc/asmHubs/commonHtml.pm - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/hubIndex.pl - lines changed 5, context: html, text, full: html, text

222404c7253a1bfc6800f8252ca698cc57e1eb0d Tue Jul 22 11:02:54 2025 -0700

• adding all "reference" sequences for RefSeq refs #29545
  • src/hg/makeDb/doc/archaeaAsmHub/archaea.orderList.tsv - lines changed 754, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 16473, context: html, text, full: html, text
  • src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 15720, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text

afe9c0bb67d2bc258825b17ae65c9a16e820d77e Tue Jul 22 12:12:38 2025 -0700

• illegal entry here for GCF_000006175.1 it is over in archaea refs #29545
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 1, context: html, text, full: html, text

054630c640462a38eb3f1cf3d2f6d7003c3ad095 Tue Jul 22 12:18:38 2025 -0700

• do not want to have T2T CHM13 exist in GenArk no redmine
  • src/hg/makeDb/doc/legacyAsmHub/promoted.list - lines changed 2, context: html, text, full: html, text

b26ad6e7a08036ee13cd05598e81dbf5111be67d Tue Jul 22 13:22:29 2025 -0700

• minimum allowed tracks on bacteria lowered and more categories allow scientific name to come through as the "common name" in the browser for odd categories of archaea and bacteria refs #29545
  • src/hg/makeDb/doc/asmHubs/commonNames.py - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh - lines changed 1, context: html, text, full: html, text

618b3efb7efbe710b1766a07f8a63d243f60fa69 Wed Jul 23 14:32:54 2025 -0700

• momentarily turn off the GenArk pushRR.sh so it can be lockfile protected from an overrun
  • src/hg/utils/otto/otto.crontab - lines changed 1, context: html, text, full: html, text

2484a9ced9c4142c547286ce90a8b6d8ee15b262 Wed Jul 23 22:59:17 2025 -0700

• adding two per user requests refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 1, context: html, text, full: html, text

61c171c4958f1ea946c88b890e7c2690cbe1b6f7 Thu Jul 24 11:19:33 2025 -0700

• adding one for demo purpose for Chris Lee refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv - lines changed 1, context: html, text, full: html, text

edbbab22e6f1006892ef64cfd0ef7e8ecd78a9c0 Thu Jul 24 21:56:47 2025 -0700

• now protecting itself from overrunning if it takes longer than a day refs #34917
  • src/hg/utils/otto/genArk/pushRR.sh - lines changed 41, context: html, text, full: html, text

73003519f1690c2731d6858b759661ad2bfa111c Thu Jul 24 21:58:13 2025 -0700

• pushRR script now protecting itself from overrunning if it takes longer than a day refs #34917
  • src/hg/utils/otto/otto.crontab - lines changed 3, context: html, text, full: html, text

98bd6fb357fb3c8922e563693f299dd498d9d27f Sat Jul 26 00:42:45 2025 -0700

• forgotten testing "head" in the size determination should not be there, no redmine
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 1, context: html, text, full: html, text

e2aceeadccb5811a593e545e1381e210b91d172c Sat Jul 26 22:11:00 2025 -0700

• adding one per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 1, context: html, text, full: html, text