File Changes for hiram

v477_base to v478_preview (2025-02-03 to 2025-02-10) v478

• src/hg/hgGateway/hgGateway.c
  • lines changed 1, context: html, text, full: html, text
    e97696bf0ffbe83d71bf11befb14a46b9134b245 Thu Feb 6 11:19:25 2025 -0800
    allow /gbdb/genark/ to serve up the GenArk hubs instead of hgdownload refs #34706
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    ea1bd03c5da8c0e084bbf39e938c25760167b03f Thu Feb 6 11:48:24 2025 -0800
    had the logic backwards on that isCuratedHubUrl function refs #34706
• src/hg/inc/hdb.h
  • lines changed 4, context: html, text, full: html, text
    20b86eabfde1a98c55bcc787d287d8c53741422c Thu Feb 6 11:20:30 2025 -0800
    allow /gbdb/genark/ to serve up the GenArk hubs instead of hgdownload refs #34706
• src/hg/js/hgGateway.js
  • lines changed 1, context: html, text, full: html, text
    e97696bf0ffbe83d71bf11befb14a46b9134b245 Thu Feb 6 11:19:25 2025 -0800
    allow /gbdb/genark/ to serve up the GenArk hubs instead of hgdownload refs #34706
• src/hg/lib/hdb.c
  • lines changed 17, context: html, text, full: html, text
    20b86eabfde1a98c55bcc787d287d8c53741422c Thu Feb 6 11:20:30 2025 -0800
    allow /gbdb/genark/ to serve up the GenArk hubs instead of hgdownload refs #34706
  • lines changed 3, context: html, text, full: html, text
    ea1bd03c5da8c0e084bbf39e938c25760167b03f Thu Feb 6 11:48:24 2025 -0800
    had the logic backwards on that isCuratedHubUrl function refs #34706
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    6a354f679c0fd5ed0ab5b4feae6d400691ad28e2 Thu Feb 6 12:10:28 2025 -0800
    this is crazy upside down logic . . . refs #34706
• src/hg/makeDb/doc/asmHubs/findEquiv.py
  • lines changed 150, context: html, text, full: html, text
    a4bf3820f12a2275c02f005c60fd84f56df26c09 Tue Feb 4 13:34:48 2025 -0800
    find GenArk equivalents given a list of accessions for Tiberius (and other data) import refs #34917
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    47ca1286ce276827df0a092c5bf3be1fbfabe1ee Tue Feb 4 13:43:03 2025 -0800
    output list in sorted order refs #34917
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 2, context: html, text, full: html, text
    49a135dcc0b53ceb23131551d47e9417fed3ac95 Mon Feb 3 17:43:20 2025 -0800
    adding 1 per user request and updating one RefSeq refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    49a135dcc0b53ceb23131551d47e9417fed3ac95 Mon Feb 3 17:43:20 2025 -0800
    adding 1 per user request and updating one RefSeq refs #29545
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    49a135dcc0b53ceb23131551d47e9417fed3ac95 Mon Feb 3 17:43:20 2025 -0800
    adding 1 per user request and updating one RefSeq refs #29545
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 6, context: html, text, full: html, text
    60273bfc304c4c57c18aa443f6fe6f96705058f9 Mon Feb 3 15:13:20 2025 -0800
    should be passing along the gff3 file to download directory - get the symLinked file here refs #35027
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 1, context: html, text, full: html, text
    08860b2a6b9377fd7deece38f70c17ae73455a64 Mon Feb 3 14:46:13 2025 -0800
    should be passing along the gff3 file to download directory - get the symLinked file here refs #35027
  • lines changed 4, context: html, text, full: html, text
    e603c24b1c5f12d0fdb9c3d8b85d93cc54599921 Mon Feb 3 15:10:57 2025 -0800
    better to make a gtf for ncbiGene like all the others refs #35027
• src/hg/utils/automation/doWindowMasker.pl
  • lines changed 75, context: html, text, full: html, text
    8d7fca788984ae4f0dde81e775574cc24bd58bbf Mon Feb 3 14:00:13 2025 -0800
    updated to new window masker binary and now bash scripts in place of the C-shell scripts no redmine