File Changes for hiram

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

• src/hg/makeDb/doc/asmHubs/commonNames.py
  • lines changed 252, 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/dynaBlatLinks.sh
  • lines changed 29, 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/gbDbLinks.sh
  • lines changed 55, 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/master.run.list
  • lines changed 15, context: html, text, full: html, text
    94040a0a0578aa64bd77590b35aab248b8b64bcb Tue Jul 23 14:41:22 2024 -0700
    refSeq update refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    94040a0a0578aa64bd77590b35aab248b8b64bcb Tue Jul 23 14:41:22 2024 -0700
    refSeq update refs #29545
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    94040a0a0578aa64bd77590b35aab248b8b64bcb Tue Jul 23 14:41:22 2024 -0700
    refSeq update refs #29545
• src/hg/makeDb/doc/hg38/470way/listOfAssembliesBirds.tsv
  • lines changed 497, 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/listOfAssembliesMammals.tsv
  • lines changed 509, 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/master.run.list
  • lines changed 2316, 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/phyloOrder.db.distance.taxId.sciName.comName.tsv
  • lines changed 469, 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/speciesTable.pl
  • lines changed 118, context: html, text, full: html, text
    4c9dc3b5a4c115f694cd3ecad26c033ebb946009 Mon Jul 22 17:50:36 2024 -0700
    script to be corrected for the 470way html table refs #34112
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    94040a0a0578aa64bd77590b35aab248b8b64bcb Tue Jul 23 14:41:22 2024 -0700
    refSeq update refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    94040a0a0578aa64bd77590b35aab248b8b64bcb Tue Jul 23 14:41:22 2024 -0700
    refSeq update refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    94040a0a0578aa64bd77590b35aab248b8b64bcb Tue Jul 23 14:41:22 2024 -0700
    refSeq update refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    94040a0a0578aa64bd77590b35aab248b8b64bcb Tue Jul 23 14:41:22 2024 -0700
    refSeq update refs #29545
• src/hg/makeDb/trackDb/human/hs1/primateChainNet.ra
  • lines changed 313, 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
  • lines changed 278, context: html, text, full: html, text
    f0939eee2c53201f05262b72ecea28ae13f53c8c Thu Jul 25 12:40:53 2024 -0700
    now with all the alignment tracks refs #34149
  • lines changed 2, 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/trackDb.ra
  • lines changed 2, 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
  • lines changed 1, 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/trackDb.chainNet.asmHub.ra
  • lines changed 96, 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