Commits for hiram

v469_preview to v469_preview2 (2024-07-22 to 2024-07-29) v469

4c9dc3b5a4c115f694cd3ecad26c033ebb946009 Mon Jul 22 17:50:36 2024 -0700

• script to be corrected for the 470way html table refs #34112
  • src/hg/makeDb/doc/hg38/470way/speciesTable.pl - lines changed 118, context: html, text, full: html, text

9dcc6d72472711ecf8b30d5350fe471c8122ec36 Mon Jul 22 17:58:48 2024 -0700

• listings used with speciesTable.pl refs #34112
  • src/hg/makeDb/doc/hg38/470way/listOfAssembliesBirds.tsv - lines changed 497, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/470way/listOfAssembliesMammals.tsv - lines changed 509, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/470way/master.run.list - lines changed 2316, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/470way/phyloOrder.db.distance.taxId.sciName.comName.tsv - lines changed 469, context: html, text, full: html, text

10628e93d4e547ae2a2d8562f87d164e86e6ce9d Tue Jul 23 12:48:08 2024 -0700

• rewrite of commonNames.pl to fix cluster home access and speed up processing refs #33720
  • src/hg/makeDb/doc/asmHubs/commonNames.py - lines changed 252, context: html, text, full: html, text

94040a0a0578aa64bd77590b35aab248b8b64bcb Tue Jul 23 14:41:22 2024 -0700

• refSeq update refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 2, context: html, text, full: html, text

f16809aeb7fd0420f7575692e352ca78054f4213 Tue Jul 23 16:35:51 2024 -0700

• scripts to make links for GenArk hubs into gbdb for potential copy to asia and euro nodes and dynamic blat backup directory refs #33526
  • src/hg/makeDb/doc/asmHubs/dynaBlatLinks.sh - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/gbDbLinks.sh - lines changed 55, context: html, text, full: html, text

29447fb02c9bd28caa60d90ed60c7ba083a934be Wed Jul 24 13:58:12 2024 -0700

• catch up definitions for chainNet track on hs1 refs #34149
  • src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra - lines changed 96, context: html, text, full: html, text

e84e5218cc7788651ae493ebea169f089b876f4e Thu Jul 25 11:54:40 2024 -0700

• starting composite track for primate chainNet on hs1 refs #34149
  • src/hg/makeDb/trackDb/human/hs1/primateChainNet.ra - lines changed 313, context: html, text, full: html, text

16fc22be4fe7fbfd45ea2dbd5daf2ed2eeb22f7a Thu Jul 25 11:55:47 2024 -0700

• starting composite track for primate chainNet on hs1 refs #34149
  • src/hg/makeDb/trackDb/human/hs1/trackDb.ra - lines changed 2, context: html, text, full: html, text

b1f9a5cb433e504204136e46f5ff83bfa25ffbbb Thu Jul 25 11:56:32 2024 -0700

• starting composite track for primate chainNet on hs1 refs #34149
  • src/hg/makeDb/trackDb/human/hs1/trackDb.ra - lines changed 1, context: html, text, full: html, text

f0939eee2c53201f05262b72ecea28ae13f53c8c Thu Jul 25 12:40:53 2024 -0700

• now with all the alignment tracks refs #34149
  • src/hg/makeDb/trackDb/human/hs1/primateChainNet.ra - lines changed 278, context: html, text, full: html, text

68804ce601cb58594713ffd8304d2a4f2987bb85 Thu Jul 25 16:25:13 2024 -0700

• do not need an s on Primate refs #34149
  • src/hg/makeDb/trackDb/human/hs1/primateChainNet.ra - lines changed 2, context: html, text, full: html, text