Commits for hiram

v459_base to v460_preview (2021-01-08 to 2024-01-16) v460

adeb22d84890dc801dfc8e7db14036feefb8b814 Mon Jan 8 21:22:57 2024 -0800

• VGP update adding 3 refs #29545
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text

8ea4174323f155bf7c9e13c5f9be3ae420c012a6 Tue Jan 9 09:04:08 2024 -0800

• VGP catchup refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 3, context: html, text, full: html, text

18ba3d5532d8357b9d568a5f1280e0bf3e25967d Tue Jan 9 10:04:44 2024 -0800

• catching up VGP primary list with GenArk refs #29545
  • src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt - lines changed 9, context: html, text, full: html, text

b0f1f612cdd0054b1061ea69ffcbe18e8fb07fc3 Tue Jan 9 11:41:15 2024 -0800

• fOsmEpe2.1 ready to go refs #29545
  • src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv - lines changed 1, context: html, text, full: html, text

b630b6031fa0a9718e8f6b2e8e9f0cff93f9ec10 Tue Jan 9 22:29:43 2024 -0800

• adding GCA_026652325.1_ASM2665232v1 Iberian ribbed newt (20211129_DDA 2022) after much trauma large genome refs #29545
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text

a92158f4897218611c25b8469aadf0d4b673a27b Wed Jan 10 08:35:56 2024 -0800

• correctly copy to dynamic blat server avoiding the repeatModeler 2bit file refs #29545
  • src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh - lines changed 3, context: html, text, full: html, text

901ed01df267d53d48309161193d3791bbc5d780 Wed Jan 10 12:40:18 2024 -0800

• alternate split procedure for large genomes in CpG Island track construction refs #29545
  • src/hg/utils/automation/doCpgIslands.pl - lines changed 105, context: html, text, full: html, text

77a819d426026e8a6ac3d7965af8f44fbb9a0272 Wed Jan 10 12:42:07 2024 -0800

• better manage large genome construction and add in RepeatModeler track refs #29545
  • src/hg/utils/automation/asmHubRmodelJoinAlign.pl - lines changed 338, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubRmskJoinAlign.pl - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 79, context: html, text, full: html, text
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 25, context: html, text, full: html, text

82a6cccdf25e3e8298cab9f78e24c9e167e3fa96 Thu Jan 11 09:44:28 2024 -0800

• mm39 to GCF_019923935.1 water buffalo lastz/chain/net complete refs #32804
  • src/hg/makeDb/doc/mm39/lastzRuns.txt - lines changed 80, context: html, text, full: html, text

be78a31ff622d9512bc04d9383ce387590882668 Sat Jan 13 13:44:12 2024 -0800

• VGP catch up GCA_028885525.1_NHGRI_mPonPyg2-v1.1-hic.freeze_alt refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - 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

73ea4a7f6eb165b33e5e9c2798e7becfc2b27bf3 Mon Jan 15 10:20:51 2024 -0800

• adding one for VGP GCA_028858805.1_NHGRI_mPanTro3-v1.1-hic.freeze_alt refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - 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