Commits for hiram

v484_preview to v484_preview2 (2025-06-16 to 2025-06-23) v484

05d27bee6baaa2a68c516dc3b2ae31841479c8e8 Wed Jun 18 13:01:40 2025 -0700

• helper script to get a hub.txt and trackDb.txt out of an existing GenArk hub refs #35898
  • src/hg/makeDb/trackDb/hubTxtFromGenArk.pl - lines changed 146, context: html, text, full: html, text

96b2dc6c40d4b9b6790fc71a5e217e275695e01f Wed Jun 18 13:58:59 2025 -0700

• initial trackDb from the GenArk hub refs #35898
  • src/hg/makeDb/trackDb/rat/rn8/genArk.trackDb.ra - lines changed 594, context: html, text, full: html, text

44d026f9ecece467941e2de29d3050689a8492f4 Wed Jun 18 14:19:46 2025 -0700

• correct spelling of descriptionUrl refs #35898
  • src/hg/makeDb/dbDbToHubTxt/dbDbToHubTxt.c - lines changed 1, context: html, text, full: html, text

0d7e402cab1ae33138f397deebe5396064a3b43a Wed Jun 18 14:28:34 2025 -0700

• now making hub.txt directly out of the GenArk hub.txt refs #35898
  • src/hg/makeDb/trackDb/maybeBuildHub - lines changed 79, context: html, text, full: html, text

083d201617a2e46b63f16cb8ee7d977fb5a7f0be Wed Jun 18 15:00:42 2025 -0700

• initial trackDb from GenArk refs #35898
  • src/hg/makeDb/trackDb/chicken/galGal7b/genArk.trackDb.ra - lines changed 896, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal7b/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal7w/genArk.trackDb.ra - lines changed 389, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal7w/trackDb.ra - lines changed 2, context: html, text, full: html, text

fa8c5189bd70f63e4e4570a6abca89ce453f4cc7 Wed Jun 18 15:01:06 2025 -0700

• initial trackDb from GenArk refs #35898
  • src/hg/makeDb/trackDb/zebrafish/danRer12/genArk.trackDb.ra - lines changed 249, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer12/trackDb.ra - lines changed 2, context: html, text, full: html, text

b8607bcc9e37304401155e66e3a87f8b6edc8035 Thu Jun 19 09:06:41 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/legacyAsmHub/legacy.clade.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 1, context: html, text, full: html, text

359adb77c8cc1ebc8f1d8013b4d138d1311b2775 Thu Jun 19 11:17:12 2025 -0700

• correct email address in the hub.txt files
  • src/hg/makeDb/doc/asmHubs/mkGenomes.pl - lines changed 2, context: html, text, full: html, text

386ada600e1f420cacee4b504ede27c63590f098 Thu Jun 19 13:20:14 2025 -0700

• mpxvRivers should be like hs1
  • src/hg/makeDb/trackDb/maybeBuildHub - lines changed 2, context: html, text, full: html, text

e8f57e6eaf7d6f0c26290eb27b2c4ee7ca139299 Thu Jun 19 15:14:38 2025 -0700

• moving this cron job from hiram account to otto account refs #34706
  • src/hg/utils/otto/genArk/pushRR/README.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/utils/otto/genArk/pushRR/alphaBetaPush.pl - lines changed 190, context: html, text, full: html, text
  • src/hg/utils/otto/genArk/pushRR/pushRR.sh - lines changed 35, context: html, text, full: html, text

c9df6cd81ece4a167f3de03888abe3522f851abf Thu Jun 19 15:29:02 2025 -0700

• adding updated HPRC assemblies refs #35415
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 101, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 101, context: html, text, full: html, text

f9a440c2466f991820f1e738522ffb83ad721d60 Fri Jun 20 11:49:03 2025 -0700

• add the Asia node pullHgwdev.sh script refs #34706
  • src/hg/utils/otto/genArk/pushRR/README.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/otto/genArk/pushRR/pullHgwdev.sh - lines changed 25, context: html, text, full: html, text

a8eae8da85b2206130a2510243b814c78ac76df3 Fri Jun 20 11:53:59 2025 -0700

• add the pushRR.sh GenArk script, used to be in Hiram\'s crontab refs #34706
  • src/hg/utils/otto/otto.crontab - lines changed 6, context: html, text, full: html, text