All File Changes

v484_preview2 to v484_base (2025-06-23 to 2025-06-30) v484

• confs/asia.hg.conf
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    e80f04ea9978518824ef5c69fbf7088f5b4a117d Sun Jun 29 01:11:16 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 5, context: html, text, full: html, text
    e80f04ea9978518824ef5c69fbf7088f5b4a117d Sun Jun 29 01:11:16 2025 -0700
    Installing updated hg.conf files from UCSC servers
• docs/index.md
  • lines changed 1, context: html, text, full: html, text
    3b69a19fd83cdcbace0acc21c321fd241f162b44 Tue Jun 24 16:37:34 2025 -0700
    Creating the Table Browser tutorial markdown, refs #35126
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    75274af9813791ce17ac135fa70f1ab8bff9e6fd Wed Jun 25 10:57:30 2025 -0700
    Removing the 'coming soon' text from the Table Browser tutorial, refs #35126
  • lines changed 1, context: html, text, full: html, text
    6d3847d1a7c65126cb2b38f631c8b8db737efdf0 Wed Jun 25 17:30:56 2025 -0700
    Making small tweaks to the new trainings, like reducing the image width to 65% so it better fits on the screen due to the resolution, and staging various updates on our pages including the news archive announcing the release of our new tutorials page, refs #35956
• docs/makefile
  • lines changed 1, context: html, text, full: html, text
    3b69a19fd83cdcbace0acc21c321fd241f162b44 Tue Jun 24 16:37:34 2025 -0700
    Creating the Table Browser tutorial markdown, refs #35126
• docs/tableBrowserTutorial.md
  • lines changed 203, context: html, text, full: html, text
    3b69a19fd83cdcbace0acc21c321fd241f162b44 Tue Jun 24 16:37:34 2025 -0700
    Creating the Table Browser tutorial markdown, refs #35126
  • lines changed 1, context: html, text, full: html, text
    6d3847d1a7c65126cb2b38f631c8b8db737efdf0 Wed Jun 25 17:30:56 2025 -0700
    Making small tweaks to the new trainings, like reducing the image width to 65% so it better fits on the screen due to the resolution, and staging various updates on our pages including the news archive announcing the release of our new tutorials page, refs #35956
• src/hg/hgBlat/hgBlat.c
  • lines changed 42, context: html, text, full: html, text
    39209bcbf0111b14b2b8aca1bb8fc245079a7226 Mon Jun 30 06:22:32 2025 -0700
    show locus name on blat results table, refs #35993
• src/hg/hgCustom/hgCustom.c
  • lines changed 1, context: html, text, full: html, text
    ebb5add03bf8711847f03e0c7183541b4b515917 Thu Jun 26 09:16:13 2025 -0700
    oops, left this out of the bedMethyl commit
• src/hg/hgGene/hgGeneData/Human/hg19/links.ra
  • lines changed 6, context: html, text, full: html, text
    ce643cc1161083650af9b97edc09d647a829b865 Fri Jun 27 15:13:25 2025 -0700
    Removing the ExonPrimer links from hgGene since the tool returns a 404 error (for hg19, hg38, mm10, mm39, mm9), refs #35989
  • lines changed 7, context: html, text, full: html, text
    dc22ea46e2f7c8783543c312cb9daa278af9c54a Mon Jun 30 12:37:04 2025 -0700
    Undoing the ExonPrimer tool removal from hgGene. Authors said they are hoping to bring it back up this week. Fixing a typo on the hg19 links.ra file too, refs #35989
• src/hg/hgGene/hgGeneData/Human/hg38/links.ra
  • lines changed 6, context: html, text, full: html, text
    ce643cc1161083650af9b97edc09d647a829b865 Fri Jun 27 15:13:25 2025 -0700
    Removing the ExonPrimer links from hgGene since the tool returns a 404 error (for hg19, hg38, mm10, mm39, mm9), refs #35989
  • lines changed 6, context: html, text, full: html, text
    dc22ea46e2f7c8783543c312cb9daa278af9c54a Mon Jun 30 12:37:04 2025 -0700
    Undoing the ExonPrimer tool removal from hgGene. Authors said they are hoping to bring it back up this week. Fixing a typo on the hg19 links.ra file too, refs #35989
• src/hg/hgGene/hgGeneData/Mouse/mm10/links.ra
  • lines changed 6, context: html, text, full: html, text
    ce643cc1161083650af9b97edc09d647a829b865 Fri Jun 27 15:13:25 2025 -0700
    Removing the ExonPrimer links from hgGene since the tool returns a 404 error (for hg19, hg38, mm10, mm39, mm9), refs #35989
  • lines changed 6, context: html, text, full: html, text
    dc22ea46e2f7c8783543c312cb9daa278af9c54a Mon Jun 30 12:37:04 2025 -0700
    Undoing the ExonPrimer tool removal from hgGene. Authors said they are hoping to bring it back up this week. Fixing a typo on the hg19 links.ra file too, refs #35989
• src/hg/hgGene/hgGeneData/Mouse/mm39/links.ra
  • lines changed 6, context: html, text, full: html, text
    ce643cc1161083650af9b97edc09d647a829b865 Fri Jun 27 15:13:25 2025 -0700
    Removing the ExonPrimer links from hgGene since the tool returns a 404 error (for hg19, hg38, mm10, mm39, mm9), refs #35989
  • lines changed 6, context: html, text, full: html, text
    dc22ea46e2f7c8783543c312cb9daa278af9c54a Mon Jun 30 12:37:04 2025 -0700
    Undoing the ExonPrimer tool removal from hgGene. Authors said they are hoping to bring it back up this week. Fixing a typo on the hg19 links.ra file too, refs #35989
• src/hg/hgGene/hgGeneData/Mouse/mm9/links.ra
  • lines changed 6, context: html, text, full: html, text
    ce643cc1161083650af9b97edc09d647a829b865 Fri Jun 27 15:13:25 2025 -0700
    Removing the ExonPrimer links from hgGene since the tool returns a 404 error (for hg19, hg38, mm10, mm39, mm9), refs #35989
  • lines changed 6, context: html, text, full: html, text
    dc22ea46e2f7c8783543c312cb9daa278af9c54a Mon Jun 30 12:37:04 2025 -0700
    Undoing the ExonPrimer tool removal from hgGene. Authors said they are hoping to bring it back up this week. Fixing a typo on the hg19 links.ra file too, refs #35989
• src/hg/hgGene/primers.c
  • lines changed 2, context: html, text, full: html, text
    ce643cc1161083650af9b97edc09d647a829b865 Fri Jun 27 15:13:25 2025 -0700
    Removing the ExonPrimer links from hgGene since the tool returns a 404 error (for hg19, hg38, mm10, mm39, mm9), refs #35989
  • lines changed 2, context: html, text, full: html, text
    dc22ea46e2f7c8783543c312cb9daa278af9c54a Mon Jun 30 12:37:04 2025 -0700
    Undoing the ExonPrimer tool removal from hgGene. Authors said they are hoping to bring it back up this week. Fixing a typo on the hg19 links.ra file too, refs #35989
• src/hg/hgGeneGraph/hgGeneGraph
  • lines changed 8, context: html, text, full: html, text
    5472f71152a9d892fc7d7081fad7e7c797d3258a Fri Jun 27 07:28:30 2025 -0700
    requiring valid user cookie to use hgGeneGraph, refs #35391
  • lines changed 1, context: html, text, full: html, text
    cde9f0ada674da7c8896a49d38645e2248eeb0b7 Mon Jun 30 06:26:21 2025 -0700
    fixing small hgGeneGraph bug, refs #35391
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 2, context: html, text, full: html, text
    77677dac32325aa1defe4bb93c775daa8f84f4a2 Fri Jun 27 09:43:39 2025 -0700
    Removing the redirect warning message which was meant to be temporary and help prevent users used to the redirect from sitting on the page indefinitely. Refs #35987
• src/hg/hgTables/mainPage.c
  • lines changed 1, context: html, text, full: html, text
    e6ab425754119a63c99092d61154bf38740fcf85 Wed Jun 25 15:30:50 2025 -0700
    Updating the note on hgTables regarding gnomAD/dbSNP data leads to a timeout, refs #35907
• src/hg/hgTracks/hgTracks.c
  • lines changed 7, context: html, text, full: html, text
    2a354509bb75e7162112bdcd5bed2f9bb02dce78 Wed Jun 25 10:48:16 2025 -0700
    Tweaking the wording to be clearer on how to make publication images, refs #29394
  • lines changed 18, context: html, text, full: html, text
    9038f4eb6850293b6fd7ca30be86637c1040c4e7 Fri Jun 27 11:55:57 2025 -0700
    Fixing issue with hideEmptySubtracks so it considers counts of all the windows in multi-region. This bug has existed since Kate added the feature. fixes #35472
• src/hg/hgTracks/simpleTracks.c
  • lines changed 21, context: html, text, full: html, text
    71a711119b542dd676e957d6d92b2b023a895492 Tue Jun 24 17:53:38 2025 -0700
    add support for bigMethyl
  • lines changed 3, context: html, text, full: html, text
    29edbac441c5813166f932eb0b5f0befa6c72aa4 Fri Jun 27 07:10:23 2025 -0700
    fixing bug with new exon mouseover code when track is not genePred, refs #35962
• src/hg/hgc/hgc.c
  • lines changed 5, context: html, text, full: html, text
    71a711119b542dd676e957d6d92b2b023a895492 Tue Jun 24 17:53:38 2025 -0700
    add support for bigMethyl
• src/hg/htdocs/cite.html
  • lines changed 1, context: html, text, full: html, text
    0661ed7af3dcfdc12b2368d62a399016e37cd049 Tue Jun 24 17:17:46 2025 -0700
    Removing extra 's', refs #35971
• src/hg/htdocs/goldenPath/help/assemblyHubGuidelines.html
  • lines changed 8, context: html, text, full: html, text
    9f28c7f69e700fa77ab91e4f4c3f3fe2432e4b8f Wed Jun 25 12:58:23 2025 -0700
    Beginning to phase our GBiB mentions for docker, refs #35611
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 9, context: html, text, full: html, text
    9f28c7f69e700fa77ab91e4f4c3f3fe2432e4b8f Wed Jun 25 12:58:23 2025 -0700
    Beginning to phase our GBiB mentions for docker, refs #35611
• src/hg/htdocs/goldenPath/help/mirror.html
  • lines changed 9, context: html, text, full: html, text
    9f28c7f69e700fa77ab91e4f4c3f3fe2432e4b8f Wed Jun 25 12:58:23 2025 -0700
    Beginning to phase our GBiB mentions for docker, refs #35611
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 2, context: html, text, full: html, text
    295fd574bb3ae393013bbf15f1df8db79b3acb27 Mon Jun 30 06:52:04 2025 -0700
    updating mirror instructions in scripts for all linux repos to add libcurl, refs #35988
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 37, context: html, text, full: html, text
    71a74c027754ea2606ca4d6bcadc73c107dc3062 Tue Jun 24 10:34:47 2025 -0700
    Announcing the release of All GENCODE for hg38, hg19 (V48), and mm39 (VM37). refs #35185 #35184 ​​#35188
  • lines changed 1, context: html, text, full: html, text
    27ad7e08d0c5752b8cc1804c5e25f075c5c7d9cf Tue Jun 24 11:47:03 2025 -0700
    Updating GENCODE V47 to V48 in the newsarch, refs #35185 #35184 #35188
  • lines changed 28, context: html, text, full: html, text
    6d3847d1a7c65126cb2b38f631c8b8db737efdf0 Wed Jun 25 17:30:56 2025 -0700
    Making small tweaks to the new trainings, like reducing the image width to 65% so it better fits on the screen due to the resolution, and staging various updates on our pages including the news archive announcing the release of our new tutorials page, refs #35956
• src/hg/htdocs/images/assemblySelection.gif
  • lines changed 0, context: html, text, full: html, text
    fa98a7f0f95ef4ae394e32db96e8ee14167dd9fd Tue Jun 24 14:06:35 2025 -0700
    Adding a gif for the assembly selction in the table Browser tutorial markdown, refs #35126
• src/hg/htdocs/images/defineRegions.gif
  • lines changed 0, context: html, text, full: html, text
    ad1333c478eef8a5a7bd7ae921789febbdd00348 Tue Jun 24 16:50:32 2025 -0700
    Adding missing GIFs for the Table Browser markdown tutorial, refs #35126
• src/hg/htdocs/images/downloadData.gif
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    ad1333c478eef8a5a7bd7ae921789febbdd00348 Tue Jun 24 16:50:32 2025 -0700
    Adding missing GIFs for the Table Browser markdown tutorial, refs #35126
• src/hg/htdocs/images/tableBrowserAnnotated.png
  • lines changed 0, context: html, text, full: html, text
    9c2e5fb2a65ece49ad485dcf552ac0bb2a63968a Tue Jun 24 16:32:22 2025 -0700
    Adding the table Browser screenshot for the markdown tutorial, refs #35126
• src/hg/htdocs/images/tableSelection.gif
  • lines changed 0, context: html, text, full: html, text
    0f41b0e7a1ea6272a0ce5d86305314ec4be6a49c Tue Jun 24 14:40:14 2025 -0700
    Replacing the large gif with two smaller ones, refs #35126
• src/hg/htdocs/images/trackSelection.gif
  • lines changed 0, context: html, text, full: html, text
    0f41b0e7a1ea6272a0ce5d86305314ec4be6a49c Tue Jun 24 14:40:14 2025 -0700
    Replacing the large gif with two smaller ones, refs #35126
• src/hg/htdocs/inc/recTrackSets.hg19.tab
  • lines changed 1, context: html, text, full: html, text
    a3b7988cbb4a1fa6c2bba2d3120fdff0889de05d Thu Jun 26 16:09:52 2025 -0700
    Fixing a typo reported by Bob, refs #35974
• src/hg/htdocs/inc/recTrackSets.hg38.tab
  • lines changed 1, context: html, text, full: html, text
    a3b7988cbb4a1fa6c2bba2d3120fdff0889de05d Thu Jun 26 16:09:52 2025 -0700
    Fixing a typo reported by Bob, refs #35974
• src/hg/htdocs/index.html
  • lines changed 4, context: html, text, full: html, text
    6d3847d1a7c65126cb2b38f631c8b8db737efdf0 Wed Jun 25 17:30:56 2025 -0700
    Making small tweaks to the new trainings, like reducing the image width to 65% so it better fits on the screen due to the resolution, and staging various updates on our pages including the news archive announcing the release of our new tutorials page, refs #35956
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    71a74c027754ea2606ca4d6bcadc73c107dc3062 Tue Jun 24 10:34:47 2025 -0700
    Announcing the release of All GENCODE for hg38, hg19 (V48), and mm39 (VM37). refs #35185 #35184 ​​#35188
  • lines changed 12, context: html, text, full: html, text
    6d3847d1a7c65126cb2b38f631c8b8db737efdf0 Wed Jun 25 17:30:56 2025 -0700
    Making small tweaks to the new trainings, like reducing the image width to 65% so it better fits on the screen due to the resolution, and staging various updates on our pages including the news archive announcing the release of our new tutorials page, refs #35956
• src/hg/htdocs/indexTraining.html
  • lines changed 1, context: html, text, full: html, text
    6d3847d1a7c65126cb2b38f631c8b8db737efdf0 Wed Jun 25 17:30:56 2025 -0700
    Making small tweaks to the new trainings, like reducing the image width to 65% so it better fits on the screen due to the resolution, and staging various updates on our pages including the news archive announcing the release of our new tutorials page, refs #35956
• src/hg/htdocs/style/HGStyle.css
  • lines changed 2, context: html, text, full: html, text
    c98e0e5941e8e94784c7b21d4246d67116c7e2a8 Fri Jun 27 11:56:37 2025 -0700
    Inversing the colors since the text is not readible with the current options, refs #35939
• src/hg/htdocs/training/index.html
  • lines changed 6, context: html, text, full: html, text
    6d3847d1a7c65126cb2b38f631c8b8db737efdf0 Wed Jun 25 17:30:56 2025 -0700
    Making small tweaks to the new trainings, like reducing the image width to 65% so it better fits on the screen due to the resolution, and staging various updates on our pages including the news archive announcing the release of our new tutorials page, refs #35956
• src/hg/inc/hgConfig.h
  • lines changed 3, context: html, text, full: html, text
    9ae100f68581af8c1a38dab93954173ef2f76254 Tue Jun 24 01:32:21 2025 -0700
    captcha user-agent exceptions are defined in hg.conf, refs #35790
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    6faaa066eb3d0d5533adc3a116fe55ae3811c33e Mon Jun 30 15:32:07 2025 -0700
    New version number v484
• src/hg/js/jquery.contextmenu.js
  • lines changed 7, context: html, text, full: html, text
    ea158e595774ba97924827663b6d19dd4d348257 Tue Jun 24 12:02:22 2025 -0700
    Fix bug introduced in last tooltips commit that un-disabled tooltips when right click menu is open, refs #34462
• src/hg/js/utils.js
  • lines changed 349, context: html, text, full: html, text
    ddfed922f22d471b014be01c3b8cc9df3ef68029 Tue Jun 24 10:24:35 2025 -0700
    Significantly simplify the mouseover code for showing tooltips on hgTracks. Use a mouseenter/leave event on each item in the image with a timer to delay showing/hiding the tooltip. The delay on the hide allows moving the mouse to the tooltip itself. Also add a mouseenter/leave event on the tooltip itself to prevent race conditions with the item events, refs #34462
  • lines changed 12, context: html, text, full: html, text
    007346754d9616c97219877c3731714eaf62c1dc Tue Jun 24 11:51:27 2025 -0700
    When encoding characters in a URL, we only want to encode characters that have not already been encoded, refs #35925
  • lines changed 11, context: html, text, full: html, text
    ea158e595774ba97924827663b6d19dd4d348257 Tue Jun 24 12:02:22 2025 -0700
    Fix bug introduced in last tooltips commit that un-disabled tooltips when right click menu is open, refs #34462
  • lines changed 3, context: html, text, full: html, text
    a70b8027e44113dc2e2ea9e27345d4f9def822c6 Mon Jun 30 12:26:39 2025 -0700
    When checking whether to not double encode url values, do not call string replace on non-string values, refs #35799
• src/hg/lib/cart.c
  • lines changed 39, context: html, text, full: html, text
    9ae100f68581af8c1a38dab93954173ef2f76254 Tue Jun 24 01:32:21 2025 -0700
    captcha user-agent exceptions are defined in hg.conf, refs #35790
  • lines changed 51, context: html, text, full: html, text
    d34f2504803125515dc89955a60ad8366bca732e Tue Jun 24 02:53:18 2025 -0700
    captcha exceptions trigger error log line, and moving curl code into lib/curlWrap.c, refs #35790
  • lines changed 19, context: html, text, full: html, text
    0beb167e80f685e0617b33a69f148a3ae1cf9d21 Mon Jun 30 05:47:37 2025 -0700
    allow alternative namedSessionDb tables, when a session was not found, refs #35992
• src/hg/lib/customFactory.c
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    38230d473a94a1376a4d813ff693ace638589939 Thu Jun 26 07:06:02 2025 -0700
    added bigMethyl custom track type
• src/hg/lib/hgConfig.c
  • lines changed 20, context: html, text, full: html, text
    9ae100f68581af8c1a38dab93954173ef2f76254 Tue Jun 24 01:32:21 2025 -0700
    captcha user-agent exceptions are defined in hg.conf, refs #35790
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    71a711119b542dd676e957d6d92b2b023a895492 Tue Jun 24 17:53:38 2025 -0700
    add support for bigMethyl
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 6, context: html, text, full: html, text
    be845a1b78879cd90c01e1f759c35f27291659f6 Tue Jun 24 14:59:49 2025 -0700
    adding some per user requests refs #29545
  • lines changed 68, context: html, text, full: html, text
    8d89132fea41fb68ad8ed1e0fe6c0ca0309816b9 Fri Jun 27 15:22:34 2025 -0700
    HPRC update refs #35415
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
  • lines changed 3, context: html, text, full: html, text
    c69c1e60152da91f9b2282ee3e3faa041309de80 Tue Jun 24 15:32:45 2025 -0700
    Eliminate gfidx indexes from downloads
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
  • lines changed 13, context: html, text, full: html, text
    306ac860b33fbb420c46eeab993b6adb740cc65b Tue Jun 24 10:16:59 2025 -0700
    Eliminate gfidx indexes from downloads
• src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
  • lines changed 18, context: html, text, full: html, text
    c69c1e60152da91f9b2282ee3e3faa041309de80 Tue Jun 24 15:32:45 2025 -0700
    Eliminate gfidx indexes from downloads
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
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    be845a1b78879cd90c01e1f759c35f27291659f6 Tue Jun 24 14:59:49 2025 -0700
    adding some per user requests refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    be845a1b78879cd90c01e1f759c35f27291659f6 Tue Jun 24 14:59:49 2025 -0700
    adding some per user requests refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    be845a1b78879cd90c01e1f759c35f27291659f6 Tue Jun 24 14:59:49 2025 -0700
    adding some per user requests refs #29545
  • lines changed 68, context: html, text, full: html, text
    8d89132fea41fb68ad8ed1e0fe6c0ca0309816b9 Fri Jun 27 15:22:34 2025 -0700
    HPRC update refs #35415
• src/hg/makeDb/trackDb/human/exonprimer.html
  • lines changed 265, context: html, text, full: html, text
    c53b1c7626e433d0511d2d430ef6f72e4eb715af Thu Jun 26 03:07:43 2025 -0700
    adding demo version of exon primers track, refs #35830
• src/hg/makeDb/trackDb/human/exonprimers.ra
  • lines changed 7, context: html, text, full: html, text
    c53b1c7626e433d0511d2d430ef6f72e4eb715af Thu Jun 26 03:07:43 2025 -0700
    adding demo version of exon primers track, refs #35830
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    df2541ccda1ddf3f89a4f908104d14c3b21b7e7a Tue Jun 24 11:19:55 2025 -0700
    Updating and adding pennantIcons for the All GENCODE tracks, refs #35185 #35184 #35188
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV47lift37.ra
  • lines changed 1, context: html, text, full: html, text
    71a74c027754ea2606ca4d6bcadc73c107dc3062 Tue Jun 24 10:34:47 2025 -0700
    Announcing the release of All GENCODE for hg38, hg19 (V48), and mm39 (VM37). refs #35185 #35184 ​​#35188
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV48lift37.ra
  • lines changed 1, context: html, text, full: html, text
    71a74c027754ea2606ca4d6bcadc73c107dc3062 Tue Jun 24 10:34:47 2025 -0700
    Announcing the release of All GENCODE for hg38, hg19 (V48), and mm39 (VM37). refs #35185 #35184 ​​#35188
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    df2541ccda1ddf3f89a4f908104d14c3b21b7e7a Tue Jun 24 11:19:55 2025 -0700
    Updating and adding pennantIcons for the All GENCODE tracks, refs #35185 #35184 #35188
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
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    df2541ccda1ddf3f89a4f908104d14c3b21b7e7a Tue Jun 24 11:19:55 2025 -0700
    Updating and adding pennantIcons for the All GENCODE tracks, refs #35185 #35184 #35188
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV47.ra
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    71a74c027754ea2606ca4d6bcadc73c107dc3062 Tue Jun 24 10:34:47 2025 -0700
    Announcing the release of All GENCODE for hg38, hg19 (V48), and mm39 (VM37). refs #35185 #35184 ​​#35188
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV48.ra
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    71a74c027754ea2606ca4d6bcadc73c107dc3062 Tue Jun 24 10:34:47 2025 -0700
    Announcing the release of All GENCODE for hg38, hg19 (V48), and mm39 (VM37). refs #35185 #35184 ​​#35188
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    df2541ccda1ddf3f89a4f908104d14c3b21b7e7a Tue Jun 24 11:19:55 2025 -0700
    Updating and adding pennantIcons for the All GENCODE tracks, refs #35185 #35184 #35188
• src/hg/makeDb/trackDb/human/revel.html
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    9233f89064f6e7154715cd0c4c893a3208b88b45 Tue Jun 24 17:07:16 2025 -0700
    Making changes from code review. Adding missing commas and moving the 19 lifted icon, refs #35968
• src/hg/makeDb/trackDb/human/trackDb.ra
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    c53b1c7626e433d0511d2d430ef6f72e4eb715af Thu Jun 26 03:07:43 2025 -0700
    adding demo version of exon primers track, refs #35830
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
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    df2541ccda1ddf3f89a4f908104d14c3b21b7e7a Tue Jun 24 11:19:55 2025 -0700
    Updating and adding pennantIcons for the All GENCODE tracks, refs #35185 #35184 #35188
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM36.ra
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    71a74c027754ea2606ca4d6bcadc73c107dc3062 Tue Jun 24 10:34:47 2025 -0700
    Announcing the release of All GENCODE for hg38, hg19 (V48), and mm39 (VM37). refs #35185 #35184 ​​#35188
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM37.ra
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    71a74c027754ea2606ca4d6bcadc73c107dc3062 Tue Jun 24 10:34:47 2025 -0700
    Announcing the release of All GENCODE for hg38, hg19 (V48), and mm39 (VM37). refs #35185 #35184 ​​#35188
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    df2541ccda1ddf3f89a4f908104d14c3b21b7e7a Tue Jun 24 11:19:55 2025 -0700
    Updating and adding pennantIcons for the All GENCODE tracks, refs #35185 #35184 #35188
• src/hg/pyLib/hgLib3.py
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    5472f71152a9d892fc7d7081fad7e7c797d3258a Fri Jun 27 07:28:30 2025 -0700
    requiring valid user cookie to use hgGeneGraph, refs #35391
• src/hg/utils/otto/otto.crontab
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    cf02fb681f98579e8cb6bc7f3caad698b1284ddf Mon Jun 30 14:25:40 2025 -0700
    Uncommenting the clinVar otto updates since it is running now, no Redmine
• src/hg/utils/otto/pubtator/BUILD
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    991e0b2cdb6c3aa152e33aa825a4f40ba161abcb Tue Jun 24 06:50:20 2025 -0700
    Adding code to convert pubtator dbSnp IDs to a track refs #35957
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• src/hg/utils/otto/pubtator/datamash_collapse.py
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    991e0b2cdb6c3aa152e33aa825a4f40ba161abcb Tue Jun 24 06:50:20 2025 -0700
    Adding code to convert pubtator dbSnp IDs to a track refs #35957
• src/hg/utils/otto/pubtator/dbs_combiner.py
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    991e0b2cdb6c3aa152e33aa825a4f40ba161abcb Tue Jun 24 06:50:20 2025 -0700
    Adding code to convert pubtator dbSnp IDs to a track refs #35957
• src/hg/utils/otto/pubtatorDbSnp/BUILD
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• src/hg/utils/otto/pubtatorDbSnp/datamash_collapse.py
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• src/hg/utils/otto/pubtatorDbSnp/dbs_combiner.py
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• src/inc/common.mk
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    65b4319455ab1c6f613eec5686677117d82d5a37 Fri Jun 27 14:09:25 2025 -0700
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• src/inc/curlWrap.h
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    d34f2504803125515dc89955a60ad8366bca732e Tue Jun 24 02:53:18 2025 -0700
    captcha exceptions trigger error log line, and moving curl code into lib/curlWrap.c, refs #35790
• src/inc/srcVersion.h
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    6faaa066eb3d0d5533adc3a116fe55ae3811c33e Mon Jun 30 15:32:07 2025 -0700
    New version number v484
• src/lib/curlWrap.c
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• src/lib/makefile
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    captcha exceptions trigger error log line, and moving curl code into lib/curlWrap.c, refs #35790
• src/parasol/inc/paraVersion.h
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    ca126a8f3bb45e369344348a2bbab6609d40a8a7 Wed Jun 25 14:15:07 2025 -0700
    Fix parasol version 12.20 so paraNodeStart passes the name in cluster.ms to the paraNode via new node option and this overrides getMachine() and so resurrect and checkJob will work correctly even for hgwdev-101.
• src/parasol/paraNode/paraNode.c
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    ca126a8f3bb45e369344348a2bbab6609d40a8a7 Wed Jun 25 14:15:07 2025 -0700
    Fix parasol version 12.20 so paraNodeStart passes the name in cluster.ms to the paraNode via new node option and this overrides getMachine() and so resurrect and checkJob will work correctly even for hgwdev-101.
• src/parasol/paraNodeStart/paraNodeStart.c
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    ca126a8f3bb45e369344348a2bbab6609d40a8a7 Wed Jun 25 14:15:07 2025 -0700
    Fix parasol version 12.20 so paraNodeStart passes the name in cluster.ms to the paraNode via new node option and this overrides getMachine() and so resurrect and checkJob will work correctly even for hgwdev-101.
• src/product/installer/README.md
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    9f28c7f69e700fa77ab91e4f4c3f3fe2432e4b8f Wed Jun 25 12:58:23 2025 -0700
    Beginning to phase our GBiB mentions for docker, refs #35611
• src/product/installer/browserSetup.sh
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    295fd574bb3ae393013bbf15f1df8db79b3acb27 Mon Jun 30 06:52:04 2025 -0700
    updating mirror instructions in scripts for all linux repos to add libcurl, refs #35988
• src/product/mirrorManual.txt
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    295fd574bb3ae393013bbf15f1df8db79b3acb27 Mon Jun 30 06:52:04 2025 -0700
    updating mirror instructions in scripts for all linux repos to add libcurl, refs #35988
• src/utils/qa/weeklybld/buildEnv.csh
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    5730636b0df37f0b9ceda20de701dad162160d6b Mon Jun 30 15:31:41 2025 -0700
    v484 final build, refs #35918
• src/utils/qa/weeklybld/buildHgCentralSql.csh
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    aa1afa2d5090721276e97be7e259c5f2b5972fd1 Mon Jun 30 15:27:39 2025 -0700
    hgdownload2 back out of rotation, no ticket
• src/utils/qa/weeklybld/checkLogins.sh
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    aa1afa2d5090721276e97be7e259c5f2b5972fd1 Mon Jun 30 15:27:39 2025 -0700
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• src/utils/qa/weeklybld/doZip.csh
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    aa1afa2d5090721276e97be7e259c5f2b5972fd1 Mon Jun 30 15:27:39 2025 -0700
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• src/utils/qa/weeklybld/makeStrictBeta.csh
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    1077002957aa20969fc78414e52fb8df8215301c Fri Jun 27 12:34:37 2025 -0700
    Making strict beta needs to make beta (for the build). Also, changes to support the use of libcurl in the utils build, since now that's linked in. refs #35988
• src/utils/qa/weeklybld/makeUserApps.csh
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    1077002957aa20969fc78414e52fb8df8215301c Fri Jun 27 12:34:37 2025 -0700
    Making strict beta needs to make beta (for the build). Also, changes to support the use of libcurl in the utils build, since now that's linked in. refs #35988
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    aa1afa2d5090721276e97be7e259c5f2b5972fd1 Mon Jun 30 15:27:39 2025 -0700
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• src/utils/qa/weeklybld/userApps.dockerfile
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    1077002957aa20969fc78414e52fb8df8215301c Fri Jun 27 12:34:37 2025 -0700
    Making strict beta needs to make beta (for the build). Also, changes to support the use of libcurl in the utils build, since now that's linked in. refs #35988
• src/utils/qa/weeklybld/userApps.sh
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    aa1afa2d5090721276e97be7e259c5f2b5972fd1 Mon Jun 30 15:27:39 2025 -0700
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• src/utils/qa/weeklybld/userAppsCheckLinking
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    1077002957aa20969fc78414e52fb8df8215301c Fri Jun 27 12:34:37 2025 -0700
    Making strict beta needs to make beta (for the build). Also, changes to support the use of libcurl in the utils build, since now that's linked in. refs #35988

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