File Changes for hiram

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

• src/hg/htdocs/goldenPath/help/api.html
  • lines changed 32, context: html, text, full: html, text
    cb718a9f9f9d2c9d43a92a618da91be0de85ed3d Mon Jul 21 16:32:16 2025 -0700
    document the findGenome endpoint and reveal the /list/genarkGenomes endpoing function refs #35468
• src/hg/makeDb/doc/archaeaAsmHub/archaea.orderList.tsv
  • lines changed 754, 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/asmHubs/commonHtml.pm
  • lines changed 11, 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/commonNames.py
  • lines changed 1, 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/hubIndex.pl
  • lines changed 5, 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/master.run.list
  • lines changed 1, context: html, text, full: html, text
    6a00887793c65562b2d7ed2f5abe5feb9dd3a7e3 Mon Jul 21 17:35:20 2025 -0700
    adding one per user request refs #29545
  • lines changed 16473, context: html, text, full: html, text
    222404c7253a1bfc6800f8252ca698cc57e1eb0d Tue Jul 22 11:02:54 2025 -0700
    adding all "reference" sequences for RefSeq refs #29545
  • lines changed 2, context: html, text, full: html, text
    2484a9ced9c4142c547286ce90a8b6d8ee15b262 Wed Jul 23 22:59:17 2025 -0700
    adding two per user requests refs #29545
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    61c171c4958f1ea946c88b890e7c2690cbe1b6f7 Thu Jul 24 11:19:33 2025 -0700
    adding one for demo purpose for Chris Lee refs #29545
  • lines changed 2, 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/verifyOnDownload.sh
  • lines changed 1, 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/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    6a00887793c65562b2d7ed2f5abe5feb9dd3a7e3 Mon Jul 21 17:35:20 2025 -0700
    adding one per user request refs #29545
  • lines changed 15720, 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/invertebrateAsmHub/invertebrate.orderList.tsv
  • 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/legacyAsmHub/legacy.clade.txt
  • lines changed 3, context: html, text, full: html, text
    6a00887793c65562b2d7ed2f5abe5feb9dd3a7e3 Mon Jul 21 17:35:20 2025 -0700
    adding one per user request refs #29545
  • 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.orderList.tsv
  • lines changed 3, 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/legacyAsmHub/promoted.list
  • lines changed 2, 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/mammalsAsmHub/mammals.orderList.tsv
  • 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/plantsAsmHub/plants.orderList.tsv
  • 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/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 1, 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/viralAsmHub/viral.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/utils/automation/doAssemblyHub.pl
  • lines changed 1, 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/otto/genArk/pushRR.sh
  • lines changed 41, 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/otto.crontab
  • 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
  • lines changed 3, 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