All File Changes

v480_preview2 to v480_base (2025-03-31 to 2025-04-07) v480

• confs/hgwdev.hg.conf
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    d7b0a4ef415e8c7bdfdd98077bc4a8165101d95e Sun Apr 6 01:11:15 2025 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 1, context: html, text, full: html, text
    2e319261249f5df2472be891cc30eb38afa515a6 Fri Apr 4 12:46:36 2025 -0700
    Scripps -> Scripps/Broad clarification in sspsygeneTimeline
• src/hg/hgHubConnect/hooks/pre-finish.c
  • lines changed 1, context: html, text, full: html, text
    d8e35c06509da9ae47bc0064f22427600844a4f3 Wed Apr 2 14:15:26 2025 -0700
    Fix cancel button not doing anything on file metadata editor, fix hub.txt upload to not create duplicate mysql rows, fix hub.txt upload to not create duplicate data-table ui rows, fix hub default name generator to not choke if a hub startsWith the default hub name but is not immediately followed by a number, refs #35383
• src/hg/hgHubConnect/trackHubWizard.c
  • lines changed 8, context: html, text, full: html, text
    60e0e2650cf3fc2f198721b5e1e58976f3a321b2 Tue Apr 1 14:14:21 2025 -0700
    Call realpath when outputting files to client in case of an incorrect hg.conf parameter with a trailing '/', refs Jairo email
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    869e1a36ed23af200ec55157d1f2a2f2aea1ea19 Thu Apr 3 13:40:40 2025 -0700
    Add search box to genome metadata field in hubSpace ui, allows searching for a genome like hgGateway, refs #31058
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 3, context: html, text, full: html, text
    7bcdb99907195a9c5eb9e4909d9d66d067addb0c Mon Mar 31 15:00:37 2025 -0700
    Fixing a spacing issue on the FAQgenes.html page, no Redmine.
  • lines changed 3, context: html, text, full: html, text
    d65389eaca84cfb6c3beb9a731ddc89c48b6fc58 Mon Mar 31 15:03:35 2025 -0700
    Moving the <p> tag before the 'Data format' to match the styling in the rest of this FAQ section. no Remdine
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    5ed62dcacb3465ebcbff8e91d32a51ac528b09bf Mon Mar 31 15:05:20 2025 -0700
    Adding a missing <p> tag, no Remdine
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 41, context: html, text, full: html, text
    b7617abed29abc5f50b1a22b1d282e043ae77a52 Mon Mar 31 15:35:38 2025 -0700
    Announcing the release of the hg38 Pseudogenes track, refs #30563
  • lines changed 2, context: html, text, full: html, text
    ff6f53780763ad8defc98f6d3f52e134024d0df5 Tue Apr 1 00:19:26 2025 -0700
    Updating the Pseudogenes newsArch track image, refs #30563
  • lines changed 2, context: html, text, full: html, text
    7ae31b7f204c16809e8c201af7a26a33bf4a20df Tue Apr 1 14:18:30 2025 -0700
    Adding more info for the grey blocks and updating the text for the color-coded pseudogene types, refs #30563
• src/hg/htdocs/images/newsArchImages/Pseudogenes.jpg
  • lines changed 0, context: html, text, full: html, text
    b7617abed29abc5f50b1a22b1d282e043ae77a52 Mon Mar 31 15:35:38 2025 -0700
    Announcing the release of the hg38 Pseudogenes track, refs #30563
• src/hg/htdocs/images/newsArchImages/PseudogenesTrack.jpg
  • lines changed 0, context: html, text, full: html, text
    ff6f53780763ad8defc98f6d3f52e134024d0df5 Tue Apr 1 00:19:26 2025 -0700
    Updating the Pseudogenes newsArch track image, refs #30563
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    b7617abed29abc5f50b1a22b1d282e043ae77a52 Mon Mar 31 15:35:38 2025 -0700
    Announcing the release of the hg38 Pseudogenes track, refs #30563
• src/hg/hubApi/tests/expected/list20.gz
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    30e5e34117e56d90af853908407e69e311a2769d Sun Mar 30 10:10:06 2025 -0700
    Random updates required for hubApi tests.
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    81917c5ea58c2240aac580ac1db41da76e2d092f Mon Mar 31 17:54:39 2025 -0700
    Last night it insisted on adding "tableBrowser" : "noGenome" to hs1 dbSNP155, but it is gone again today.
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    e098cb8665bc2a1c4fb45698a985a6f77dfcf1b5 Mon Mar 31 19:06:22 2025 -0700
    oops, I forgot to run make in hg/makedb/trackdb first. Now it is good.
• src/hg/hubApi/tests/expected/list22.gz
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    30e5e34117e56d90af853908407e69e311a2769d Sun Mar 30 10:10:06 2025 -0700
    Random updates required for hubApi tests.
• src/hg/hubApi/tests/expected/redmine23733.gz
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    30e5e34117e56d90af853908407e69e311a2769d Sun Mar 30 10:10:06 2025 -0700
    Random updates required for hubApi tests.
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    fea1f3f76d3ef7d052d3b8790ff1dbd3e79491fe Mon Mar 31 18:13:50 2025 -0700
    More mysterious changes since last night, ask Hiram or QA.
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    e098cb8665bc2a1c4fb45698a985a6f77dfcf1b5 Mon Mar 31 19:06:22 2025 -0700
    oops, I forgot to run make in hg/makedb/trackdb first. Now it is good.
• src/hg/hubApi/tests/expected/schema06.gz
  • lines changed 0, context: html, text, full: html, text
    30e5e34117e56d90af853908407e69e311a2769d Sun Mar 30 10:10:06 2025 -0700
    Random updates required for hubApi tests.
  • lines changed 0, context: html, text, full: html, text
    fea1f3f76d3ef7d052d3b8790ff1dbd3e79491fe Mon Mar 31 18:13:50 2025 -0700
    More mysterious changes since last night, ask Hiram or QA.
  • lines changed 0, context: html, text, full: html, text
    e098cb8665bc2a1c4fb45698a985a6f77dfcf1b5 Mon Mar 31 19:06:22 2025 -0700
    oops, I forgot to run make in hg/makedb/trackdb first. Now it is good.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    4e801961d8639c42956fb5455f9f537f24ba4e1d Mon Apr 7 13:14:06 2025 -0700
    New version number v480
• src/hg/js/autocompleteCat.js
  • lines changed 5, context: html, text, full: html, text
    869e1a36ed23af200ec55157d1f2a2f2aea1ea19 Thu Apr 3 13:40:40 2025 -0700
    Add search box to genome metadata field in hubSpace ui, allows searching for a genome like hgGateway, refs #31058
• src/hg/js/hgMyData.js
  • lines changed 17, context: html, text, full: html, text
    2729e45f862a7cade4d2c107ba9c1adc395c3e79 Tue Apr 1 13:39:46 2025 -0700
    Dont parse a missing fileList variable. Warn the user that their hub name or file name they are creating has invalid characters before submission so they can edit them sooner, refs Jairo email
  • lines changed 5, context: html, text, full: html, text
    d8e35c06509da9ae47bc0064f22427600844a4f3 Wed Apr 2 14:15:26 2025 -0700
    Fix cancel button not doing anything on file metadata editor, fix hub.txt upload to not create duplicate mysql rows, fix hub.txt upload to not create duplicate data-table ui rows, fix hub default name generator to not choke if a hub startsWith the default hub name but is not immediately followed by a number, refs #35383
  • lines changed 145, context: html, text, full: html, text
    869e1a36ed23af200ec55157d1f2a2f2aea1ea19 Thu Apr 3 13:40:40 2025 -0700
    Add search box to genome metadata field in hubSpace ui, allows searching for a genome like hgGateway, refs #31058
• src/hg/js/tutorials/gatewayTutorial.js
  • lines changed 122, context: html, text, full: html, text
    a89d2c4aa3a3c6462db0f6d964463f26d0d9a48c Thu Apr 3 17:19:29 2025 -0700
    Adding the gateway tutorial js file, refs #35464
• src/hg/lib/userdata.c
  • lines changed 12, context: html, text, full: html, text
    d8e35c06509da9ae47bc0064f22427600844a4f3 Wed Apr 2 14:15:26 2025 -0700
    Fix cancel button not doing anything on file metadata editor, fix hub.txt upload to not create duplicate mysql rows, fix hub.txt upload to not create duplicate data-table ui rows, fix hub default name generator to not choke if a hub startsWith the default hub name but is not immediately followed by a number, refs #35383
• src/hg/makeDb/doc/asmHubs/asmHubList.pl
  • lines changed 5, context: html, text, full: html, text
    f7738bbbaf7e4795de4aca61f476d1ddfe127e21 Sun Apr 6 22:00:59 2025 -0700
    reset scripts to function on hgdownload3 no redmine
• src/hg/makeDb/doc/asmHubs/genArkFileList.sh
  • lines changed 23, context: html, text, full: html, text
    f9604ebe649761abff816536cc309d813b32bc34 Sun Apr 6 21:57:55 2025 -0700
    script running on the hgdownload machines to general file list of all GenArk hub files on hgdownload no redmine
• src/hg/makeDb/doc/asmHubs/hubIndex.pl
  • lines changed 6, context: html, text, full: html, text
    f7738bbbaf7e4795de4aca61f476d1ddfe127e21 Sun Apr 6 22:00:59 2025 -0700
    reset scripts to function on hgdownload3 no redmine
• src/hg/makeDb/doc/asmHubs/hubList.sh
  • lines changed 41, context: html, text, full: html, text
    f7738bbbaf7e4795de4aca61f476d1ddfe127e21 Sun Apr 6 22:00:59 2025 -0700
    reset scripts to function on hgdownload3 no redmine
• src/hg/makeDb/doc/asmHubs/lastzRuns.txt
  • lines changed 166, context: html, text, full: html, text
    0b1eaa046425cf42843abc6fd9fbf4a7e2d696a0 Mon Apr 7 09:22:03 2025 -0700
    adding several alignments, refs #35465
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 43, context: html, text, full: html, text
    c85c734dd97a76942a9f73af2b37d4ad526203c2 Wed Apr 2 16:56:00 2025 -0700
    VGP update refs #29545
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    49d34002ae6baa02bb112d539e4e2995e455f088 Fri Apr 4 01:52:38 2025 -0700
    VGP update adding a couple refs #29545
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    30a730a1899e9687cfd677f9f3bb4fd705309d3b Sat Apr 5 07:53:28 2025 -0700
    VGP update adding some mammals refs #29545
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    f98767fe73fb191bc64ca09b97b947a740c94645 Sun Apr 6 18:46:35 2025 -0700
    BRC update adding 122 virus genomes refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 7, context: html, text, full: html, text
    c85c734dd97a76942a9f73af2b37d4ad526203c2 Wed Apr 2 16:56:00 2025 -0700
    VGP update refs #29545
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    49d34002ae6baa02bb112d539e4e2995e455f088 Fri Apr 4 01:52:38 2025 -0700
    VGP update adding a couple refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 8, context: html, text, full: html, text
    c85c734dd97a76942a9f73af2b37d4ad526203c2 Wed Apr 2 16:56:00 2025 -0700
    VGP update refs #29545
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    49d34002ae6baa02bb112d539e4e2995e455f088 Fri Apr 4 01:52:38 2025 -0700
    VGP update adding a couple refs #29545
• src/hg/makeDb/doc/hg38/encode4.txt
  • lines changed 47, context: html, text, full: html, text
    994049f75b593264f0ff047f88903468bf1c2031 Fri Apr 4 13:35:35 2025 -0700
    mm10 and hg38 encode4
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
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    c85c734dd97a76942a9f73af2b37d4ad526203c2 Wed Apr 2 16:56:00 2025 -0700
    VGP update refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 4, context: html, text, full: html, text
    c85c734dd97a76942a9f73af2b37d4ad526203c2 Wed Apr 2 16:56:00 2025 -0700
    VGP update refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    c85c734dd97a76942a9f73af2b37d4ad526203c2 Wed Apr 2 16:56:00 2025 -0700
    VGP update refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 18, context: html, text, full: html, text
    c85c734dd97a76942a9f73af2b37d4ad526203c2 Wed Apr 2 16:56:00 2025 -0700
    VGP update refs #29545
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    30a730a1899e9687cfd677f9f3bb4fd705309d3b Sat Apr 5 07:53:28 2025 -0700
    VGP update adding some mammals refs #29545
• src/hg/makeDb/doc/mm10.txt
  • lines changed 46, context: html, text, full: html, text
    994049f75b593264f0ff047f88903468bf1c2031 Fri Apr 4 13:35:35 2025 -0700
    mm10 and hg38 encode4
• src/hg/makeDb/doc/mm39/lastzRuns.txt
  • lines changed 85, context: html, text, full: html, text
    84655d205f74a77b773c1b25e89a42e37d913158 Sat Apr 5 17:03:53 2025 -0700
    mm39 to platypus (GCF_004115215.2) lastz/chain/net run for user, refs #35448
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    c85c734dd97a76942a9f73af2b37d4ad526203c2 Wed Apr 2 16:56:00 2025 -0700
    VGP update refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
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    c85c734dd97a76942a9f73af2b37d4ad526203c2 Wed Apr 2 16:56:00 2025 -0700
    VGP update refs #29545
  • lines changed 2, context: html, text, full: html, text
    49d34002ae6baa02bb112d539e4e2995e455f088 Fri Apr 4 01:52:38 2025 -0700
    VGP update adding a couple refs #29545
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 130, context: html, text, full: html, text
    f98767fe73fb191bc64ca09b97b947a740c94645 Sun Apr 6 18:46:35 2025 -0700
    BRC update adding 122 virus genomes refs #29545
• src/hg/makeDb/outside/encode4/gtfToBed.py
  • lines changed 176, context: html, text, full: html, text
    994049f75b593264f0ff047f88903468bf1c2031 Fri Apr 4 13:35:35 2025 -0700
    mm10 and hg38 encode4
• src/hg/makeDb/trackDb/human/hg38/encode4.html
  • lines changed 62, context: html, text, full: html, text
    994049f75b593264f0ff047f88903468bf1c2031 Fri Apr 4 13:35:35 2025 -0700
    mm10 and hg38 encode4
• src/hg/makeDb/trackDb/human/hg38/encode4.ra
  • lines changed 16, context: html, text, full: html, text
    994049f75b593264f0ff047f88903468bf1c2031 Fri Apr 4 13:35:35 2025 -0700
    mm10 and hg38 encode4
• src/hg/makeDb/trackDb/human/hg38/pseudogenes.html
  • lines changed 7, context: html, text, full: html, text
    7ae31b7f204c16809e8c201af7a26a33bf4a20df Tue Apr 1 14:18:30 2025 -0700
    Adding more info for the grey blocks and updating the text for the color-coded pseudogene types, refs #30563
• src/hg/makeDb/trackDb/human/hg38/pseudogenes.ra
  • lines changed 1, context: html, text, full: html, text
    b7617abed29abc5f50b1a22b1d282e043ae77a52 Mon Mar 31 15:35:38 2025 -0700
    Announcing the release of the hg38 Pseudogenes track, refs #30563
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    994049f75b593264f0ff047f88903468bf1c2031 Fri Apr 4 13:35:35 2025 -0700
    mm10 and hg38 encode4
• src/hg/makeDb/trackDb/mouse/mm10/encode4.html
  • lines changed 62, context: html, text, full: html, text
    994049f75b593264f0ff047f88903468bf1c2031 Fri Apr 4 13:35:35 2025 -0700
    mm10 and hg38 encode4
• src/hg/makeDb/trackDb/mouse/mm10/encode4.ra
  • lines changed 16, context: html, text, full: html, text
    994049f75b593264f0ff047f88903468bf1c2031 Fri Apr 4 13:35:35 2025 -0700
    mm10 and hg38 encode4
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    994049f75b593264f0ff047f88903468bf1c2031 Fri Apr 4 13:35:35 2025 -0700
    mm10 and hg38 encode4
• src/hg/makeDb/trackDb/patchTracks.new.ra
  • lines changed 2, context: html, text, full: html, text
    2afb0b02aca7612ab8dc1bc6c7751eacd16f5c59 Thu Apr 3 09:32:12 2025 -0700
    Adding Alignment Gap/Insertion Display settings for the GRC Patches composite track that are default in both Fix Patches and Alt Haplotypes track, refs #35326
• src/hg/utils/findCutters/findCutters.c
  • lines changed 1, context: html, text, full: html, text
    181319a8467865af984e1b3980ff5124f7a31d6c Mon Mar 31 15:30:14 2025 -0700
    Fixes for bad slNameSort override in findCutters util. refs #26947
• src/hg/utils/findCutters/makefile
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    181319a8467865af984e1b3980ff5124f7a31d6c Mon Mar 31 15:30:14 2025 -0700
    Fixes for bad slNameSort override in findCutters util. refs #26947
• src/hg/utils/otto/lrg/lrgWrapper.sh
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    cb1c4abd76722d2f3dc7e767022b7b812573ec5a Wed Apr 2 16:40:10 2025 -0700
    Updating the cron since the , is causing issues, No RM
• src/inc/srcVersion.h
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    4e801961d8639c42956fb5455f9f537f24ba4e1d Mon Apr 7 13:14:06 2025 -0700
    New version number v480
• src/utils/qa/assemblyStatsCron.py
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    ae16b2213a7c8fd157250ca9753dade44d7c2671 Fri Apr 4 11:32:59 2025 -0700
    Since tabFmt was committed to the tree in the new hgwdev, it needs a stdin designation when used in pipes to work. No RM.
• src/utils/qa/checkHTTPS
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    4c08e95f2e342747adc45d6af6a3d70d4242c440 Tue Apr 1 14:47:42 2025 -0700
    Removing hgdownload-euro.soe.ucsc.edu since Erich shares that is redundant to genome-euro.ucsc.edu, No RM
• src/utils/qa/weeklybld/buildEnv.csh
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    9cbe07274e58dd306ffde53b3f393129f49d9fc5 Mon Apr 7 13:13:30 2025 -0700
    v480 final build, refs #35440
• src/utils/qa/weeklybld/buildHgCentralSql.csh
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    11a265a818ac6a4437ac9e007beccdd83ad8a416 Mon Apr 7 13:09:40 2025 -0700
    hgdownload2 re-enters the rotation, as does a new hgdownload3, no ticket
• src/utils/qa/weeklybld/checkLogins.sh
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    11a265a818ac6a4437ac9e007beccdd83ad8a416 Mon Apr 7 13:09:40 2025 -0700
    hgdownload2 re-enters the rotation, as does a new hgdownload3, no ticket
• src/utils/qa/weeklybld/doZip.csh
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    11a265a818ac6a4437ac9e007beccdd83ad8a416 Mon Apr 7 13:09:40 2025 -0700
    hgdownload2 re-enters the rotation, as does a new hgdownload3, no ticket
• src/utils/qa/weeklybld/makeUserApps.csh
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    11a265a818ac6a4437ac9e007beccdd83ad8a416 Mon Apr 7 13:09:40 2025 -0700
    hgdownload2 re-enters the rotation, as does a new hgdownload3, no ticket
• src/utils/qa/weeklybld/userApps.sh
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    11a265a818ac6a4437ac9e007beccdd83ad8a416 Mon Apr 7 13:09:40 2025 -0700
    hgdownload2 re-enters the rotation, as does a new hgdownload3, no ticket

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• files changed: 78