Commits for hiram

v492_base to v493_preview (2025-12-15 to 2026-01-12) v493

6120d02a6aa7faf052299967d8bace2d2d706ad3 Mon Dec 15 13:06:28 2025 -0800

• one additional color code definition for paralogous annotations refs #35776
  • src/hg/makeDb/trackDb/TOGAv2.html - lines changed 5, context: html, text, full: html, text

06dd761c2c6ddc53e7e191203da75569b1c1cb9c Mon Dec 15 13:11:12 2025 -0800

• adding TOGAv2 refs #35776
  • src/hg/makeDb/trackDb/betaGenArk.txt - lines changed 1, context: html, text, full: html, text

d425930659b77acd38c14eaefda720d52da1ddc1 Mon Dec 15 16:28:32 2025 -0800

• more detail on these push procedures
  • src/hg/utils/otto/genArk/README - lines changed 117, context: html, text, full: html, text

e17a685b61034584686ffa679916f6b3373a9c05 Wed Dec 17 10:07:07 2025 -0800

• adding --mkpath to the rsync for the contrib directory since it can be multiple levels deep refs #35776
  • src/hg/utils/otto/genArk/quickPush.pl - lines changed 1, context: html, text, full: html, text

a5855ded640de30881d63cf3255399cc3c8e4238 Sat Dec 20 12:44:18 2025 -0800

• fixup empty lav result for axt output per Michael Hiller
  • src/hg/utils/automation/blastz-run-ucsc - lines changed 9, context: html, text, full: html, text

6b4d4242132b637c7ae9a2da8d63efea608d41af Mon Dec 22 18:51:50 2025 -0800

• get the liftOver and quickLift links properly in place for both database and GenArk browsers and the entries into the liftOverChain and quickLiftChain tables
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 49, context: html, text, full: html, text

334039f0943574d0c1d988b016b6052ff0a09228 Tue Dec 23 21:13:03 2025 -0800

• adding a couple per user requests refs #29545
  • src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 1, 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/mammalsAsmHub/mammals.orderList.tsv - lines changed 1, context: html, text, full: html, text

bd4e8fdfa8af70460de2f21bb3555a93331d4e88 Fri Dec 26 12:51:22 2025 -0800

• RefSeq update refs #29545
  • src/hg/makeDb/doc/archaeaAsmHub/archaea.orderList.tsv - lines changed 39, context: html, text, full: html, text
  • src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 487, context: html, text, full: html, text
  • 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 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv - lines changed 39, context: html, text, full: html, text

3ffb2a7935a31d3dc7d1c43de0386cd4e3369863 Mon Jan 5 15:59:21 2026 -0800

• fix error in path name for beta push refs #35776
  • src/hg/utils/otto/genArk/quickPush.pl - lines changed 1, context: html, text, full: html, text

419c9b44aca638612f184d11f406c6d01269e01f Tue Jan 6 09:42:11 2026 -0800

• do not update groups.txt if it remains identical to template source refs #29545
  • src/hg/makeDb/doc/asmHubs/mkGenomes.pl - lines changed 9, context: html, text, full: html, text

1f57795eeb934d739cb4b3050a0484f29dd50fec Tue Jan 6 14:33:57 2026 -0800

• try out the VEuPathDB and TOGAv2 tracks refs #35778 #35776
  • src/hg/makeDb/trackDb/publicGenArk.txt - lines changed 2, context: html, text, full: html, text

74421edfd8c8e930e3bc90e86f87c7dab8031e95 Wed Jan 7 09:23:34 2026 -0800

• correct name on buildDir
  • src/hg/utils/automation/doFasTAN.pl - lines changed 2, context: html, text, full: html, text