Commits for hiram

v486_preview to v486_preview2 (2025-07-28 to 2025-08-04) v486

372119b197658e6d7ba8b25a1a6ac653c09e605a Mon Jul 28 10:31:00 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/birdsAsmHub/birds.orderList.tsv - lines changed 1, context: html, text, full: html, text

31801be892b78fcf34ef81581e24c33b920c306a Mon Jul 28 15:06:21 2025 -0700

• adding several per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text

312be12573fb0c4823e6e30ef5a58e10ae604f8c Wed Jul 30 15:30:07 2025 -0700

• new scripts to replace pushRR.sh and alphaBetaPush.pl for dramatic performance improvement refs #34917
  • src/hg/utils/otto/genArk/pushNewOnes.sh - lines changed 63, context: html, text, full: html, text
  • src/hg/utils/otto/genArk/quickPush.pl - lines changed 377, context: html, text, full: html, text

25232ea095a9222e0c63a940d12557ca6db6122c Wed Jul 30 15:34:46 2025 -0700

• remove the testing grep -v statement refs #34917
  • src/hg/utils/otto/genArk/quickPush.pl - lines changed 7, context: html, text, full: html, text

4fe9ce6537fbfad528c0e2c20e7d6ee36e3729fd Wed Jul 30 15:40:54 2025 -0700

• the cron job that makes the dev.todaylist.gz listing refs #34917
  • src/hg/utils/otto/genArk/devList.sh - lines changed 29, context: html, text, full: html, text

ec439df2d702798e3b36edfe7faa47ddafab5521 Wed Jul 30 15:44:28 2025 -0700

• add note about this otto cron job refs #34917
  • src/hg/utils/otto/genArk/devList.sh - lines changed 12, context: html, text, full: html, text

5ae22064718499c7c5341f9846e43e56e66a1e21 Wed Jul 30 15:46:28 2025 -0700

• adding the devList.sh script for GenArk pushing reference refs #34917
  • src/hg/utils/otto/otto.crontab - lines changed 3, context: html, text, full: html, text

cbe6c4ccb2a229070c54d068798b567d3801b604 Thu Jul 31 11:08:32 2025 -0700

• safety check on validity of directory path refs #34917
  • src/hg/utils/otto/genArk/pushNewOnes.sh - lines changed 21, context: html, text, full: html, text

ac52c1b6f5b37ede7efe9748d8cb2a57cab8d2ad Thu Jul 31 11:31:50 2025 -0700

• now running new and improved scripts that are much more efficient refs #34917
  • src/hg/utils/otto/genArk/pushRR.sh - lines changed 31, context: html, text, full: html, text

72dbdcd6baa45774ed51ce6640d2cb19c7f5c583 Thu Jul 31 15:12:01 2025 -0700

• add in assembly alias names in the "description" so they can also be matched refs #33720
  • src/hg/hubApi/assemblyList.py - lines changed 58, context: html, text, full: html, text

c08b66512ffda6f2cf43bd3687a68f710965d08f Thu Jul 31 17:04:18 2025 -0700

• using hgLoadMafSummary.v483 to work around maf dots no redmine
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 2, context: html, text, full: html, text

e58683ce4249ec43684a323144f88ca8e56d14a1 Thu Jul 31 17:11:53 2025 -0700

• using hgLoadMafSummary.v483 to work around maf dots no redmine
  • src/hg/utils/automation/doRecipBest.pl - lines changed 1, context: html, text, full: html, text

d016d8f62aac199e12ae92583784e426b22a1c14 Fri Aug 1 10:38:15 2025 -0700

• catch up to current script with automatic repeat masker identification and email complete message refs #23891
  • src/hg/makeDb/doc/asmHubs/runBuild - lines changed 166, context: html, text, full: html, text

967d0f8de69dce6f67490147438aec1164015b76 Fri Aug 1 10:48:48 2025 -0700

• make public.hub.txt and hub.txt have the same mtime to avoid duplicate pushing in the otto cron jobs refs #34917
  • src/hg/makeDb/doc/asmHubs/mkGenomes.pl - lines changed 7, context: html, text, full: html, text

79631bad98a7a3a016f29a35ff1fe0e48dbccf11 Fri Aug 1 22:52:14 2025 -0700

• BRC update refs #34337
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 74, context: html, text, full: html, text
  • src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 69, context: html, text, full: html, text
  • src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv - lines changed 31, context: html, text, full: html, text