File Changes for hiram

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v482_preview2 to v482_base (2025-05-13 to 2025-05-19) v482

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src/hg/htdocs/assemblyRequest.html
- lines changed 10, context: html, text, full: html, text
  d6861d8f0eb72ab5fd3b940f25193934101e7033 Fri May 16 10:58:13 2025 -0700
  redirect page for this obsolete function to the new search page refs #32596
src/hg/makeDb/doc/asmHubs/master.run.list
- lines changed 1, context: html, text, full: html, text
  a2b64b9d2358a5e6ec6c6dbfac102bd78fb27663 Tue May 13 16:03:08 2025 -0700
  adding one per user request refs #29545
- lines changed 1, context: html, text, full: html, text
  5c843d25210930c1fd699e23f1632cf2b6b25067 Wed May 14 11:04:21 2025 -0700
  adding one per user request refs #29545
- lines changed 1, context: html, text, full: html, text
  170c79270978a2686a58e91657412b99596299e5 Fri May 16 10:40:23 2025 -0700
  adding one per user request refs #34337
src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
- lines changed 21, context: html, text, full: html, text
  cfd801899529a9a9b0db3cc408a8f5e3c6ecb670 Thu May 15 13:24:49 2025 -0700
  implement a scientific name override system to fixup names for F1 hybrid diploid assemblies refsd #34917
src/hg/makeDb/doc/asmHubs/mkGenomes.pl
- lines changed 5, context: html, text, full: html, text
  1c297cf2b02d635690955ac09b5a915a7b8e54d5 Wed May 14 12:07:41 2025 -0700
  write out an information file about which assemblies have chain/net tracks "hasChainNets.txt" refs #34917
- lines changed 97, context: html, text, full: html, text
  8859fbf8a8d7408df039c9ab29c8b3bdeb225516 Wed May 14 12:09:07 2025 -0700
  now writing out beta.hub.txt and public.hub.txt based on control from trackDb listings publicGenArk.txt and betaGenArk.txt refs #34917
- lines changed 2, context: html, text, full: html, text
  f4cc4c7a53b4b1c33e5f83bc7e82b5145e7971b6 Thu May 15 13:33:45 2025 -0700
  correct blank lines in track stanzas in the public and beta hub.txt files refs #34917
src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
- lines changed 33, context: html, text, full: html, text
  cfd801899529a9a9b0db3cc408a8f5e3c6ecb670 Thu May 15 13:24:49 2025 -0700
  implement a scientific name override system to fixup names for F1 hybrid diploid assemblies refsd #34917
src/hg/makeDb/doc/asmHubs/sciNameOverride.txt
- lines changed 22, context: html, text, full: html, text
  cfd801899529a9a9b0db3cc408a8f5e3c6ecb670 Thu May 15 13:24:49 2025 -0700
  implement a scientific name override system to fixup names for F1 hybrid diploid assemblies refsd #34917
src/hg/makeDb/doc/asmHubs/trackData.pl
- lines changed 21, context: html, text, full: html, text
  cfd801899529a9a9b0db3cc408a8f5e3c6ecb670 Thu May 15 13:24:49 2025 -0700
  implement a scientific name override system to fixup names for F1 hybrid diploid assemblies refsd #34917
src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
- lines changed 1, context: html, text, full: html, text
  b6b05dad3475c3c668e83e70968380be5c767daf Fri May 16 10:39:43 2025 -0700
  new low track count for BRC project refs #34337
src/hg/makeDb/doc/brcAsmHub/brc.orderList.tsv
- lines changed 197, context: html, text, full: html, text
  e9ab99078ff5a3b1d8bc80002ed57f6400c3ec51 Fri May 16 07:17:04 2025 -0700
  catching up to BRC project list refs #34337
src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
- lines changed 1, context: html, text, full: html, text
  5c843d25210930c1fd699e23f1632cf2b6b25067 Wed May 14 11:04:21 2025 -0700
  adding one per user request refs #29545
- lines changed 6, context: html, text, full: html, text
  fd2acb99619aee5e48bd79c9de487b43236079f2 Thu May 15 13:46:54 2025 -0700
  correct common names on the F1 haploid assemblies refs #34370
- lines changed 10, context: html, text, full: html, text
  b38b615425ec779eb4fdb2135fe34c8cc6b8c9ad Thu May 15 15:21:07 2025 -0700
  common name fixups to match VGP listings refs 34370
- lines changed 1, context: html, text, full: html, text
  170c79270978a2686a58e91657412b99596299e5 Fri May 16 10:40:23 2025 -0700
  adding one per user request refs #34337
src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
- lines changed 4, context: html, text, full: html, text
  fd2acb99619aee5e48bd79c9de487b43236079f2 Thu May 15 13:46:54 2025 -0700
  correct common names on the F1 haploid assemblies refs #34370
src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
- lines changed 1, context: html, text, full: html, text
  a2b64b9d2358a5e6ec6c6dbfac102bd78fb27663 Tue May 13 16:03:08 2025 -0700
  adding one per user request refs #29545
src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
- lines changed 8, context: html, text, full: html, text
  c2a768a6f781c36cc2fcfff8f59da94b021ac7d6 Thu May 15 15:11:22 2025 -0700
  common name fixups to match VGP listings refs 34370
- lines changed 2, context: html, text, full: html, text
  6f8f116800e9cfef3f3f80883a8d0690bedaa556 Thu May 15 15:24:13 2025 -0700
  common name fixups to match VGP listings refs 34370
src/hg/makeDb/trackDb/betaGenArk.txt
- lines changed 4, context: html, text, full: html, text
  ed2e2fa8c95fd33065539210e89cc7decb12998f Wed May 14 12:02:09 2025 -0700
  adding genark beta and public track control listings refs #34917
src/hg/makeDb/trackDb/contrib/tiberius/Tiberius.html
- lines changed 11, context: html, text, full: html, text
  f86d097e1dac55d91a23830697808108abad9a00 Thu May 15 13:28:01 2025 -0700
  html and trackDb for contributed Tiberius gene tracks refs #34917
src/hg/makeDb/trackDb/contrib/tiberius/tiberius.trackDb.txt
- lines changed 12, context: html, text, full: html, text
  f86d097e1dac55d91a23830697808108abad9a00 Thu May 15 13:28:01 2025 -0700
  html and trackDb for contributed Tiberius gene tracks refs #34917
src/hg/makeDb/trackDb/publicGenArk.txt
- lines changed 4, context: html, text, full: html, text
  ed2e2fa8c95fd33065539210e89cc7decb12998f Wed May 14 12:02:09 2025 -0700
  adding genark beta and public track control listings refs #34917
src/hg/utils/otto/genArk/alphaBetaPush.pl
- lines changed 186, context: html, text, full: html, text
  5ee6a100c664a51ff24ae10ae7779bbe3b506603 Wed May 14 15:31:08 2025 -0700
  now managing the push of beta and public versions of hub.txt files for contrib tracks in genark browsers refs #34917
- lines changed 9, context: html, text, full: html, text
  f35500dabcf4527f5a1a482d4e0da03c44f01f63 Thu May 15 14:03:05 2025 -0700
  correctly rsync only in the case where the contrib/track directory does actually exist refs #35917
src/hg/utils/otto/genArk/pushRR.sh
- lines changed 15, context: html, text, full: html, text
  5ee6a100c664a51ff24ae10ae7779bbe3b506603 Wed May 14 15:31:08 2025 -0700
  now managing the push of beta and public versions of hub.txt files for contrib tracks in genark browsers refs #34917

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