File Changes for hiram

v471_base to v472_preview (2024-09-16 to 2024-09-23) v472

• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 16, context: html, text, full: html, text
    730f1cb766d7ab79175fc0c27f88e8139cdb9a60 Fri Sep 20 12:05:47 2024 -0700
    customized text for index page on BRC project (these custom headers should instead be header.html in the project source directories) and now sending out assemblyList.json file refs #34337
• src/hg/makeDb/doc/asmHubs/hubIndex.pl
  • lines changed 13, context: html, text, full: html, text
    3a91c81cd956cef5e7400591771598dfc88b7833 Fri Sep 20 12:09:16 2024 -0700
    now with BRC project refs #34337
  • lines changed 1, context: html, text, full: html, text
    b80f130bdfeb72f4600c82a8f8c41730eaaf1c9e Fri Sep 20 12:14:10 2024 -0700
    allow function on hgdownload2 also refs #34337
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 91, context: html, text, full: html, text
    d901c4001373c5e8250a933a64129fc899538529 Tue Sep 17 08:42:49 2024 -0700
    adding 92 for BRC update refs #34337
  • lines changed 85, context: html, text, full: html, text
    b1c4322ae696e98901ec40b96ff7682c4cdf5414 Sat Sep 21 15:38:39 2024 -0700
    BRC update adding 85 refs #34337
  • lines changed 3, context: html, text, full: html, text
    b5a6af80774e1d90b4189b4cad6a46eed169aaf3 Mon Sep 23 10:09:45 2024 -0700
    BRC update refs #34337
• src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
  • lines changed 23, context: html, text, full: html, text
    730f1cb766d7ab79175fc0c27f88e8139cdb9a60 Fri Sep 20 12:05:47 2024 -0700
    customized text for index page on BRC project (these custom headers should instead be header.html in the project source directories) and now sending out assemblyList.json file refs #34337
• src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
  • lines changed 27, context: html, text, full: html, text
    730f1cb766d7ab79175fc0c27f88e8139cdb9a60 Fri Sep 20 12:05:47 2024 -0700
    customized text for index page on BRC project (these custom headers should instead be header.html in the project source directories) and now sending out assemblyList.json file refs #34337
• src/hg/makeDb/doc/asmHubs/trackData.pl
  • lines changed 23, context: html, text, full: html, text
    730f1cb766d7ab79175fc0c27f88e8139cdb9a60 Fri Sep 20 12:05:47 2024 -0700
    customized text for index page on BRC project (these custom headers should instead be header.html in the project source directories) and now sending out assemblyList.json file refs #34337
• src/hg/makeDb/doc/asmHubs/tsvToJson.py
  • lines changed 68, context: html, text, full: html, text
    5c3fb7c203029aae27a69a7104b690b30da7f558 Mon Sep 23 13:05:57 2024 -0700
    fixup to allow UCSC database names and reading dbGcaGcf.tsf to get GCA GCF accessions on those UCSC names refs #34337
• src/hg/makeDb/doc/brcAsmHub/brc.orderList.tsv
  • lines changed 90, context: html, text, full: html, text
    869ed52c9ded4eaa7f4b0c3532833d35eda9cd81 Mon Sep 16 15:57:41 2024 -0700
    adding another 90 mostly protozoa and parasitic alveolates. refs #34337
  • lines changed 49, context: html, text, full: html, text
    118e84d39b5450677f01c78a63a248839ed53487 Thu Sep 19 13:05:48 2024 -0700
    BRC update adding 49 refs #34337
  • lines changed 26, context: html, text, full: html, text
    6852e815f318d1fdcde50022a5b6eafb630cde97 Mon Sep 23 11:06:03 2024 -0700
    update adding 27 assemblies refs #34337
  • lines changed 3, context: html, text, full: html, text
    f78731cb5cf3c346e08194bfadc4765122ca1031 Mon Sep 23 13:22:37 2024 -0700
    using mm39 and hg38 for mouse and human standard references refs #34337
• src/hg/makeDb/doc/brcAsmHub/dbGcaGcf.tsv
  • lines changed 3, context: html, text, full: html, text
    f78731cb5cf3c346e08194bfadc4765122ca1031 Mon Sep 23 13:22:37 2024 -0700
    using mm39 and hg38 for mouse and human standard references refs #34337
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 16, context: html, text, full: html, text
    27a34b2d1472b7a8dc28631fa09423dc875b1153 Thu Sep 19 12:44:12 2024 -0700
    BRC update refs #34337
  • lines changed 28, context: html, text, full: html, text
    b5a6af80774e1d90b4189b4cad6a46eed169aaf3 Mon Sep 23 10:09:45 2024 -0700
    BRC update refs #34337
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 55, context: html, text, full: html, text
    27a34b2d1472b7a8dc28631fa09423dc875b1153 Thu Sep 19 12:44:12 2024 -0700
    BRC update refs #34337
  • lines changed 28, context: html, text, full: html, text
    b5a6af80774e1d90b4189b4cad6a46eed169aaf3 Mon Sep 23 10:09:45 2024 -0700
    BRC update refs #34337
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 30, context: html, text, full: html, text
    27a34b2d1472b7a8dc28631fa09423dc875b1153 Thu Sep 19 12:44:12 2024 -0700
    BRC update refs #34337
  • lines changed 15, context: html, text, full: html, text
    6f8907ff0e4a54c394521dbb4219d40fd98822d2 Thu Sep 19 15:05:38 2024 -0700
    eliminate items that should not be here refs #34337
  • lines changed 2, context: html, text, full: html, text
    503c713ebcfd7ca50d0f9427c0b8b91642a231da Mon Sep 23 10:12:09 2024 -0700
    BRC update refs #34337
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 17, context: html, text, full: html, text
    27a34b2d1472b7a8dc28631fa09423dc875b1153 Thu Sep 19 12:44:12 2024 -0700
    BRC update refs #34337
  • lines changed 2, context: html, text, full: html, text
    503c713ebcfd7ca50d0f9427c0b8b91642a231da Mon Sep 23 10:12:09 2024 -0700
    BRC update refs #34337
• src/hg/makeDb/doc/zoonomiaAsmHub/dbGcaGcf.tsv
  • lines changed 6, context: html, text, full: html, text
    5c3fb7c203029aae27a69a7104b690b30da7f558 Mon Sep 23 13:05:57 2024 -0700
    fixup to allow UCSC database names and reading dbGcaGcf.tsf to get GCA GCF accessions on those UCSC names refs #34337
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 1, context: html, text, full: html, text
    ffce6032dc038a0b9e45af61b3fa3a3032568dc2 Mon Sep 16 15:39:28 2024 -0700
    do not need altColor on track ncbiRefSeq causes red wings on chevrons in NCBI RefSeq "all" track no redmine
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 10, context: html, text, full: html, text
    4f6ea1808067647f43b31a4ed3e55723129de2f9 Fri Sep 20 19:05:36 2024 -0700
    genome-source has now become githubusercontent refs #34449
• src/hg/utils/automation/doNcbiRefSeq.pl
  • lines changed 3, context: html, text, full: html, text
    95ee44a5d737970678a6d856d1228b908941de2c Fri Sep 20 19:00:51 2024 -0700
    genome-source has now become githubusercontent refs #34449
  • lines changed 1, context: html, text, full: html, text
    6a74ea5eb50dd8b835d28650e1b235bb38245a02 Sun Sep 22 12:58:11 2024 -0700
    correct quote for githubusercontent reference refs #34449
• src/utils/qa/weeklybld/sendLogEmail.pl
  • lines changed 6, context: html, text, full: html, text
    7a0bb6ac0281a3d8193816821e9e7b6c27d93763 Tue Sep 17 12:29:48 2024 -0700
    correctly recognize authors case insensitive no redmine;