All File Changes

v488_base to v489_preview (2025-09-22 to 2025-09-29) v489

• confs/asia.hg.conf
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    e195c2f36763631c5985c734ff6d1334e3e4c8db Sun Sep 28 01:11:19 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 3, context: html, text, full: html, text
    e195c2f36763631c5985c734ff6d1334e3e4c8db Sun Sep 28 01:11:19 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 1, context: html, text, full: html, text
    e195c2f36763631c5985c734ff6d1334e3e4c8db Sun Sep 28 01:11:19 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    e195c2f36763631c5985c734ff6d1334e3e4c8db Sun Sep 28 01:11:19 2025 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 6, context: html, text, full: html, text
    697565bdd3b78419adda01dd9b709c6bf1a6503d Mon Sep 29 13:54:15 2025 -0700
    Removing tilde which caused mermaid code display issue
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    44646e64fea6a1522b78399dbb41354d11345b5c Tue Sep 23 15:42:40 2025 -0700
    Fixing the hot keys. Refs #35667
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 1, context: html, text, full: html, text
    f50fbe16a5fe95c1e0c1a84e88b689f06e9c682f Fri Sep 26 17:46:49 2025 -0700
    Replacing the Assembly Hub wiki links with the new Assembly Hub User Guide page, refs #34740
• src/hg/htdocs/admin/filePicker.html
  • lines changed 97, context: html, text, full: html, text
    520322178ed1029edc43b6b998023ba84d083301 Fri Sep 19 21:36:28 2025 -0700
    Better error handling (hopefully) on page refresh.
  • lines changed 1, context: html, text, full: html, text
    9b015ea745e001ab48af46610af1b7724fd066cc Mon Sep 22 16:28:40 2025 -0700
    Typo in filepicker text
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 6, context: html, text, full: html, text
    13e0fcf19a6d71108ecb13289c09de4c1286780c Fri Sep 26 14:27:58 2025 -0700
    Fixing broken links reported by the student interns, refs #36072
  • lines changed 4, context: html, text, full: html, text
    f50fbe16a5fe95c1e0c1a84e88b689f06e9c682f Fri Sep 26 17:46:49 2025 -0700
    Replacing the Assembly Hub wiki links with the new Assembly Hub User Guide page, refs #34740
• src/hg/htdocs/goldenPath/help/hubBasics.html
  • lines changed 381, context: html, text, full: html, text
    6e51c97b0bc6b5a95059f53c95c0478563c96650 Mon Sep 22 14:07:01 2025 -0700
    adding new simplified hub help page, refs #29810
• src/hg/htdocs/goldenPath/help/hubQuickStart.html
  • lines changed 2, context: html, text, full: html, text
    f50fbe16a5fe95c1e0c1a84e88b689f06e9c682f Fri Sep 26 17:46:49 2025 -0700
    Replacing the Assembly Hub wiki links with the new Assembly Hub User Guide page, refs #34740
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 8, context: html, text, full: html, text
    f50fbe16a5fe95c1e0c1a84e88b689f06e9c682f Fri Sep 26 17:46:49 2025 -0700
    Replacing the Assembly Hub wiki links with the new Assembly Hub User Guide page, refs #34740
• src/hg/htdocs/goldenPath/help/hubQuickStartGroups.html
  • lines changed 2, context: html, text, full: html, text
    f50fbe16a5fe95c1e0c1a84e88b689f06e9c682f Fri Sep 26 17:46:49 2025 -0700
    Replacing the Assembly Hub wiki links with the new Assembly Hub User Guide page, refs #34740
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 1, context: html, text, full: html, text
    f50fbe16a5fe95c1e0c1a84e88b689f06e9c682f Fri Sep 26 17:46:49 2025 -0700
    Replacing the Assembly Hub wiki links with the new Assembly Hub User Guide page, refs #34740
• src/hg/htdocs/goldenPath/help/publicHubGuidelines.html
  • lines changed 1, context: html, text, full: html, text
    f50fbe16a5fe95c1e0c1a84e88b689f06e9c682f Fri Sep 26 17:46:49 2025 -0700
    Replacing the Assembly Hub wiki links with the new Assembly Hub User Guide page, refs #34740
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 30, context: html, text, full: html, text
    a3f49ed673a655dd78777fa8b45fed9aaa0c4e2c Wed Sep 24 13:53:31 2025 -0700
    Releasing and announcing the Panmask Easy 151b Regions track, refs #36293
  • lines changed 29, context: html, text, full: html, text
    f605a32582341e556d53451a4ccc5c63e75a8fc5 Wed Sep 24 15:56:30 2025 -0700
    Staging the CoLoRSdb announcement and fixing a merge conflict, refs #34120
  • lines changed 14, context: html, text, full: html, text
    630550c8e3eef4679f6cfb1e89af12c1a05875d5 Wed Sep 24 18:00:04 2025 -0700
    Adding an image to the news post. Fixing the g= parameter for the hs1 assembly, refs #34120
  • lines changed 1, context: html, text, full: html, text
    068dc3da618e5c90dc3380622faa7a8e83a89bcb Wed Sep 24 18:03:14 2025 -0700
    Adding a link to the indexNews page. Fixing the title of the post, refs #34120
  • lines changed 2, context: html, text, full: html, text
    5172b8655d2ef742e9bf918cedb3fa746d50d0f0 Thu Sep 25 11:21:58 2025 -0700
    Uncommenting the Panmask track newsarch announcement, refs #36293
  • lines changed 7, context: html, text, full: html, text
    a6e1b8d8399b6f62b8b02d4082437caeb452fa42 Thu Sep 25 15:38:08 2025 -0700
    Fixing typos and differences between the track description page and the mouseOver tooltip, refs #36405
• src/hg/htdocs/images/bigBedCommonSettings.png
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    6e51c97b0bc6b5a95059f53c95c0478563c96650 Mon Sep 22 14:07:01 2025 -0700
    adding new simplified hub help page, refs #29810
• src/hg/htdocs/images/bigBedCommonSettingsPopUp.png
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    6e51c97b0bc6b5a95059f53c95c0478563c96650 Mon Sep 22 14:07:01 2025 -0700
    adding new simplified hub help page, refs #29810
• src/hg/htdocs/images/bigBedReqSettings.png
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    6e51c97b0bc6b5a95059f53c95c0478563c96650 Mon Sep 22 14:07:01 2025 -0700
    adding new simplified hub help page, refs #29810
• src/hg/htdocs/images/bigWigReqSettings.png
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    6e51c97b0bc6b5a95059f53c95c0478563c96650 Mon Sep 22 14:07:01 2025 -0700
    adding new simplified hub help page, refs #29810
• src/hg/htdocs/images/compositeBigWig.png
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    6e51c97b0bc6b5a95059f53c95c0478563c96650 Mon Sep 22 14:07:01 2025 -0700
    adding new simplified hub help page, refs #29810
• src/hg/htdocs/images/newsArchImages/CoLoRSdb.png
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    92289d88fce4aa4595b103e1422a8cc68f2c9225 Wed Sep 24 17:46:32 2025 -0700
    Adding an image for the CoLoRSdb track, refs #34120
• src/hg/htdocs/images/newsArchImages/panmask.png
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    615c6d8c4ad795a59e0127d750409a13f4a9b988 Wed Sep 24 13:56:21 2025 -0700
    Adding image for the Panmask Easy 151b Regions track announcement, refs #36293
• src/hg/htdocs/images/superTrackEx.png
  • lines changed 0, context: html, text, full: html, text
    6e51c97b0bc6b5a95059f53c95c0478563c96650 Mon Sep 22 14:07:01 2025 -0700
    adding new simplified hub help page, refs #29810
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    a3f49ed673a655dd78777fa8b45fed9aaa0c4e2c Wed Sep 24 13:53:31 2025 -0700
    Releasing and announcing the Panmask Easy 151b Regions track, refs #36293
  • lines changed 13, context: html, text, full: html, text
    068dc3da618e5c90dc3380622faa7a8e83a89bcb Wed Sep 24 18:03:14 2025 -0700
    Adding a link to the indexNews page. Fixing the title of the post, refs #34120
  • lines changed 2, context: html, text, full: html, text
    5172b8655d2ef742e9bf918cedb3fa746d50d0f0 Thu Sep 25 11:21:58 2025 -0700
    Uncommenting the Panmask track newsarch announcement, refs #36293
• src/hg/htdocs/training/index.html
  • lines changed 1, context: html, text, full: html, text
    f50fbe16a5fe95c1e0c1a84e88b689f06e9c682f Fri Sep 26 17:46:49 2025 -0700
    Replacing the Assembly Hub wiki links with the new Assembly Hub User Guide page, refs #34740
• src/hg/js/hgHubConnect.js
  • lines changed 3, context: html, text, full: html, text
    2062c2da5318c4ccec237e9e099c97e447a52f06 Thu Sep 25 17:08:39 2025 -0700
    Don't do hubSpace init if we are looking at a different hgHubConnect tab, call hubSpace init when we switch to that tab, refs Jairo email
• src/hg/js/hgMyData.js
  • lines changed 6, context: html, text, full: html, text
    82addf257c3e62738dc588cc36382286354b7274 Thu Sep 25 16:11:56 2025 -0700
    Warn hubspace users that the feature is only available over https, refs Jairo email
  • lines changed 4, context: html, text, full: html, text
    2062c2da5318c4ccec237e9e099c97e447a52f06 Thu Sep 25 17:08:39 2025 -0700
    Don't do hubSpace init if we are looking at a different hgHubConnect tab, call hubSpace init when we switch to that tab, refs Jairo email
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    b14d21d38541d5cd49b58db365a216670f061b55 Fri Sep 26 10:53:28 2025 -0700
    Clarify that it is only hubspace that is unavailable over plain http
  • lines changed 9, context: html, text, full: html, text
    7ebf31ae4ac969f75b0adbce330572c3fa86cf60 Fri Sep 26 11:18:44 2025 -0700
    Keep track of hubspace UI initialization, and only do it on the first tab switch to the hub upload tab. After switching tabs we don't need to keep re-initting
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    922f56ae7feb0e0b3b8a5ffe31b9384d604440b2 Fri Sep 26 12:10:39 2025 -0700
    Do not allow plus or dash chars in hubspace filenames or hub names to prevent url encoding issues, refs Jairo email
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    5fbd341691cc520c5d274e50373797de05de9262 Tue Sep 23 13:28:19 2025 -0700
    Remove 0-width characters before calling encodeURIComponent on hgTracks search box, refs #36387
• src/hg/js/igv.min.js
  • lines changed 9, context: html, text, full: html, text
    1bafe5a5569d58aa2446c60ef2a42f531d47698f Sun Sep 21 21:56:30 2025 -0700
    igv dialog position fixes. Misc minor cleanup
• src/hg/js/igvFileHelper.js
  • lines changed 238, context: html, text, full: html, text
    520322178ed1029edc43b6b998023ba84d083301 Fri Sep 19 21:36:28 2025 -0700
    Better error handling (hopefully) on page refresh.
  • lines changed 9, context: html, text, full: html, text
    0aba57c06e4263f91f5b1e20eafca36946b4649b Sat Sep 20 21:31:02 2025 -0700
    remove local igvBrowser variable for clarity. igvBrowser is a global
  • lines changed 22, context: html, text, full: html, text
    1bafe5a5569d58aa2446c60ef2a42f531d47698f Sun Sep 21 21:56:30 2025 -0700
    igv dialog position fixes. Misc minor cleanup
  • lines changed 8, context: html, text, full: html, text
    5035e5c42aaae212c7f0d5bf9455349143af4d31 Sun Sep 21 22:00:59 2025 -0700
    Show message to user if clicking 'Add IGV Tracks' with an open file picker
  • lines changed 43, context: html, text, full: html, text
    b9c90b025f5cc6cefe1fa0347293ce5000446988 Sun Sep 21 23:38:22 2025 -0700
    Delay inserting IGV row until dom content is loaded. Inserting the row before the image table is ready sends the browser into a race condition that requires completely closing and restarting. It's not 100% sure that waiting for a dom content load event will fix this.
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    5ba5f5e316b0df66963ecd7f1415844c6fff0ea5 Mon Sep 22 10:42:53 2025 -0700
    Add alert informing user to use file manager window to add tracks.
  • lines changed 2, context: html, text, full: html, text
    6ba04af6275e48f59d4f9d9e731ea4fdec143874 Mon Sep 22 22:40:50 2025 -0700
    Whitespace fixes
• src/hg/js/parallelSegments.js
  • lines changed 446, context: html, text, full: html, text
    a5989b86cf7627764874340dbf1bb70d287f4890 Wed Sep 24 06:43:10 2025 -0700
    removing parallelSegments.js
• src/hg/js/utils.js
  • lines changed 10, context: html, text, full: html, text
    af507965b2d219779285784fe96f37c78bab19c4 Mon Sep 29 13:04:27 2025 -0700
    Make mouseover on gear icon trigger the same mouseover as without the gear icon, refs #36232
• src/hg/lib/userdata.c
  • lines changed 35, context: html, text, full: html, text
    aa0273b99929f6d4c9d4a46589d2c9c9b72b98b5 Tue Sep 23 10:29:45 2025 -0700
    Fix hubspace deletion when files are on a different filesystem: when deleting the row from the hgcentral table, we look up the filename by a string that needs the original filesystem path, so one, for safety check that the location we are trying to delete exists before issuing the delete command, and two, unswap the dataDir prefix and delete based off of that if the swapped location is not in the table, refs #31058
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    bc37197a054d2768bf4174cb0b7081ec90a0e315 Wed Sep 24 09:28:52 2025 -0700
    Oops forgot arguments in last commit, refs build email
• src/hg/makeDb/doc/archaeaAsmHub/archaea.orderList.tsv
  • lines changed 19, context: html, text, full: html, text
    c6fd1904cfe78f6b1fd6090de058af19338e1d45 Sat Sep 27 20:41:29 2025 -0700
    RefSeq update adding a set refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    b4ed79f52844e55287e25f88dd0179bab388f14c Sat Sep 27 20:11:55 2025 -0700
    up to date with some user requests refs #29545
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    78e3ba81556f4d74c6b1db6d13181628dc9eb5a2 Sat Sep 27 20:43:42 2025 -0700
    RefSeq update adding a set refs #29545
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    8b041dfd940cb119c147c8b168816e34eb2beee4 Sat Sep 27 20:27:43 2025 -0700
    adding two per user request refs #29545
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    56bf935d1ca4c490b5fcffa315565810e2dfe0c6 Sat Sep 27 20:44:06 2025 -0700
    RefSeq update adding a set refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    185c41196deb6af93af9600b16ef18df675b9b04 Sat Sep 27 20:44:43 2025 -0700
    RefSeq update adding a set refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
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    f8da5806964bf17f0210528569118d05cf12b30b Sat Sep 27 20:36:15 2025 -0700
    RefSeq update adding a couple refs #29545
• src/hg/makeDb/doc/ucscGenes/hg19.gencodeV49lift37.sh
  • lines changed 23, context: html, text, full: html, text
    9503a0661f3e9d5c1a265bff94d958076d0f1d8c Mon Sep 29 12:53:12 2025 -0700
    Makedoc for knownGene V49lift37, refs #36167
• src/hg/makeDb/doc/ucscGenes/hg38.gencodeV49.sh
  • lines changed 37, context: html, text, full: html, text
    2d78f7651d5a78740cf16d032e2fc702a3e24342 Mon Sep 29 00:11:16 2025 -0700
    knownGeneV49 makedoc, refs #36169
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    88bb629bad0b8ca30fc964ec32f8751589a26410 Sat Sep 27 20:37:33 2025 -0700
    RefSeq update adding a couple refs #29545
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 34, context: html, text, full: html, text
    0f360180366caea00a5f9050c01f84c9cb8d51a6 Sat Sep 27 20:45:11 2025 -0700
    RefSeq update adding a set refs #29545
• src/hg/makeDb/trackDb/human/colorsDb.html
  • lines changed 129, context: html, text, full: html, text
    46fb2ffff6cdf0a620ff9ab18fc86d0f7f1d7806 Wed Sep 24 17:30:46 2025 -0700
    Staging the CoLoRSdb track for hg38 and hs1, refs #34120
• src/hg/makeDb/trackDb/human/colorsDb.ra
  • lines changed 38, context: html, text, full: html, text
    46fb2ffff6cdf0a620ff9ab18fc86d0f7f1d7806 Wed Sep 24 17:30:46 2025 -0700
    Staging the CoLoRSdb track for hg38 and hs1, refs #34120
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    c03ba0968b302fb6cf026140fe0d8816fda7f6a1 Thu Sep 25 13:57:37 2025 -0700
    Editing the long and short labels based on Anna's feedback, refs #34120
• src/hg/makeDb/trackDb/human/decipher.ra
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    a6e1b8d8399b6f62b8b02d4082437caeb452fa42 Thu Sep 25 15:38:08 2025 -0700
    Fixing typos and differences between the track description page and the mouseOver tooltip, refs #36405
• src/hg/makeDb/trackDb/human/decipherContainer.html
  • lines changed 7, context: html, text, full: html, text
    a6e1b8d8399b6f62b8b02d4082437caeb452fa42 Thu Sep 25 15:38:08 2025 -0700
    Fixing typos and differences between the track description page and the mouseOver tooltip, refs #36405
• src/hg/makeDb/trackDb/human/hg19/knownGene.alpha.ra
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    535fdd04a3ab8f4dc566b81eca9af50064492bfa Mon Sep 29 12:13:17 2025 -0700
    V49lift37 knownGene trackDb
• src/hg/makeDb/trackDb/human/hg19/knownGeneArchive.ra
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    535fdd04a3ab8f4dc566b81eca9af50064492bfa Mon Sep 29 12:13:17 2025 -0700
    V49lift37 knownGene trackDb
• src/hg/makeDb/trackDb/human/hg19/knownGeneV49lift37.html
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    535fdd04a3ab8f4dc566b81eca9af50064492bfa Mon Sep 29 12:13:17 2025 -0700
    V49lift37 knownGene trackDb
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    535fdd04a3ab8f4dc566b81eca9af50064492bfa Mon Sep 29 12:13:17 2025 -0700
    V49lift37 knownGene trackDb
• src/hg/makeDb/trackDb/human/hg38/knownGeneArchive.ra
  • lines changed 29, context: html, text, full: html, text
    100a103b5311c0c22fd2aa3705b366da08542198 Sun Sep 28 23:59:52 2025 -0700
    V49 knownGene trackDb
• src/hg/makeDb/trackDb/human/hg38/knownGeneV49.html
  • lines changed 168, context: html, text, full: html, text
    100a103b5311c0c22fd2aa3705b366da08542198 Sun Sep 28 23:59:52 2025 -0700
    V49 knownGene trackDb
• src/hg/makeDb/trackDb/human/hg38/problematic.ra
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    a3f49ed673a655dd78777fa8b45fed9aaa0c4e2c Wed Sep 24 13:53:31 2025 -0700
    Releasing and announcing the Panmask Easy 151b Regions track, refs #36293
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    100a103b5311c0c22fd2aa3705b366da08542198 Sun Sep 28 23:59:52 2025 -0700
    V49 knownGene trackDb
• src/hg/makeDb/trackDb/human/spliceAIWt.ra
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    a175eacba8400b62327e4cd27e3a3b53a0c7d3a3 Tue Sep 23 19:59:10 2025 -0700
    forgot setting the boundaries of spliceAiWt track, refs #35100
• src/hg/makeDb/trackDb/human/structuralVariants.html
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    46fb2ffff6cdf0a620ff9ab18fc86d0f7f1d7806 Wed Sep 24 17:30:46 2025 -0700
    Staging the CoLoRSdb track for hg38 and hs1, refs #34120
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    46fb2ffff6cdf0a620ff9ab18fc86d0f7f1d7806 Wed Sep 24 17:30:46 2025 -0700
    Staging the CoLoRSdb track for hg38 and hs1, refs #34120
• src/hg/utils/otto/clinvar/clinVarToBed
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    4d06b1e359477194ed8b3e50dfec23aa695396af Wed Sep 24 10:53:20 2025 -0700
    Commiting changes from the clinVarToBed utility that was running on /hive to the kent source tree, no Redmine
• src/hg/utils/otto/otto.crontab
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    4c06071f44d989e9e20b7b896b717a65c3040deb Mon Sep 22 17:08:13 2025 -0700
    Adding cronjob for Cell Browser that updates facets .json files.
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    7ebf86ace6ddda4200ba4e481d12ad7e0ae67a78 Wed Sep 24 14:11:29 2025 -0700
    Adding missing cd statement and fixing file not found error

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• files changed: 84