All File Changes

v486_preview to v486_preview2 (2025-07-28 to 2025-08-04) v486

• confs/asia.hg.conf
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    5569016ae987f9b3c1f5af9973b6fdd15a7ee2fb Sun Aug 3 01:11:18 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 2, context: html, text, full: html, text
    5569016ae987f9b3c1f5af9973b6fdd15a7ee2fb Sun Aug 3 01:11:18 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/preview.hg.conf
  • lines changed 2, context: html, text, full: html, text
    5569016ae987f9b3c1f5af9973b6fdd15a7ee2fb Sun Aug 3 01:11:18 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 11, context: html, text, full: html, text
    5569016ae987f9b3c1f5af9973b6fdd15a7ee2fb Sun Aug 3 01:11:18 2025 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 5, context: html, text, full: html, text
    063c7a647ab64823205f94600da0b549b502b1ea Mon Jul 28 15:30:49 2025 -0700
    Collapsing Yale Aim Gene lists for readability and marking done the 29 NDD genes item ADGC3_I_7, 2025-04-01
  • lines changed 6, context: html, text, full: html, text
    dd8d056c5e4d059305de5c9ab86441284efd845a Tue Jul 29 09:37:39 2025 -0700
    Collapsing Yale Aim3 milestones [ADGC3_M_22 , ADGC3_N_23] for readability
• src/hg/hgConvert/hgConvert.c
  • lines changed 6, context: html, text, full: html, text
    214fe5d147954cd0d62f127025f7cb3a59f38085 Fri Aug 1 15:26:14 2025 -0700
    support Genark hubs as fromDb in hgConvert
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    84688c95e385ee526a59d7dac8f6ff644781361b Sat Aug 2 11:11:57 2025 -0700
    ongoing work on quickLift. Made saved sessions work a little more rationally
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    509dafad770b5483a9a6efe709c4b83017dd1d29 Sun Aug 3 12:28:59 2025 -0700
    always ask if user wants to lift annotation in hgConvert if the config variable is on
• src/hg/hgHubConnect/hooks/pre-finish.c
  • lines changed 13, context: html, text, full: html, text
    4a55f1d55a77c2c3a1e3e5b08d1efb369535d859 Fri Aug 1 15:14:31 2025 -0700
    Prevent bug in tusd pre-finish hook where the hub.txt and container directory had the correct locations but the actual uploaded file had a symlinked location, which was throwing off the UI code that strips off the dataDir portion of the location
• src/hg/hgTables/bedMethyl.c
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    216fa1001e5c2c6dfed06c0ed18592acf4b94c32 Tue Jul 29 10:23:35 2025 -0700
    take out commented out include files
• src/hg/hgTracks/wigTrack.c
  • lines changed 4, context: html, text, full: html, text
    fcc66292648958c70053054587910f187ba249d0 Mon Jul 28 15:42:35 2025 -0700
    make setColorWith work a big less weirdly by using an invisible color for the graph when there is nothing in the bigBed.
• src/hg/htdocs/goldenPath/help/bedMethyl.html
  • lines changed 2, context: html, text, full: html, text
    23bea12e98867f3cd6b931d0537c68b57a2f0503 Thu Jul 31 10:54:57 2025 -0700
    Incorporating Lou's feedback to bedMethyl.html and announcing the bedMethyl/bigMethyl type, refs #36002
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 4, context: html, text, full: html, text
    60787421e3e9ac5591b9957cf91f409f39b45a78 Mon Jul 28 17:21:24 2025 -0700
    Adding windowingFunction on advice to prevent strange coloring when using setColorWith setting while zoomed out, refs #36070
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 34, context: html, text, full: html, text
    23bea12e98867f3cd6b931d0537c68b57a2f0503 Thu Jul 31 10:54:57 2025 -0700
    Incorporating Lou's feedback to bedMethyl.html and announcing the bedMethyl/bigMethyl type, refs #36002
  • lines changed 18, context: html, text, full: html, text
    e69a819c8711dd9fe6f8e475e1591ea41516106f Fri Aug 1 13:09:47 2025 -0700
    Announcing the PubTator track for hg38 and hg19, refs #35957
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    23bea12e98867f3cd6b931d0537c68b57a2f0503 Thu Jul 31 10:54:57 2025 -0700
    Incorporating Lou's feedback to bedMethyl.html and announcing the bedMethyl/bigMethyl type, refs #36002
  • lines changed 12, context: html, text, full: html, text
    e69a819c8711dd9fe6f8e475e1591ea41516106f Fri Aug 1 13:09:47 2025 -0700
    Announcing the PubTator track for hg38 and hg19, refs #35957
• src/hg/hubApi/assemblyList.py
  • lines changed 58, context: html, text, full: html, text
    72dbdcd6baa45774ed51ce6640d2cb19c7f5c583 Thu Jul 31 15:12:01 2025 -0700
    add in assembly alias names in the "description" so they can also be matched refs #33720
• src/hg/inc/userdata.h
  • lines changed 8, context: html, text, full: html, text
    685a30331929add5218e4cae8dcff9fef35e9a0a Thu Jul 31 15:46:11 2025 -0700
    Feedback from code review and hgw0 testing of hubspace. If the hubspace filesystem is mounted, do the replacement in the dataDir string when first setting the dataDir (code review). Later, when stripping the dataDir off the filename to print in the UI, add a check for the mount point so we can correctly strip off the right string from the incoming filename, which will have a different path prefix than on the hbuspace machine.
• src/hg/js/utils.js
  • lines changed 2, context: html, text, full: html, text
    6d4317bf9b64c4aebc8aae6563287a455e4054cb Thu Jul 31 15:50:29 2025 -0700
    Fixup new gear and x icons to use proper tooltips, refs #36152
• src/hg/lib/cart.c
  • lines changed 2, context: html, text, full: html, text
    84688c95e385ee526a59d7dac8f6ff644781361b Sat Aug 2 11:11:57 2025 -0700
    ongoing work on quickLift. Made saved sessions work a little more rationally
• src/hg/lib/hubConnect.c
  • lines changed 12, context: html, text, full: html, text
    84688c95e385ee526a59d7dac8f6ff644781361b Sat Aug 2 11:11:57 2025 -0700
    ongoing work on quickLift. Made saved sessions work a little more rationally
• src/hg/lib/quickLift.c
  • lines changed 3, context: html, text, full: html, text
    84688c95e385ee526a59d7dac8f6ff644781361b Sat Aug 2 11:11:57 2025 -0700
    ongoing work on quickLift. Made saved sessions work a little more rationally
• src/hg/lib/trackHub.c
  • lines changed 13, context: html, text, full: html, text
    84688c95e385ee526a59d7dac8f6ff644781361b Sat Aug 2 11:11:57 2025 -0700
    ongoing work on quickLift. Made saved sessions work a little more rationally
• src/hg/lib/userdata.c
  • lines changed 45, context: html, text, full: html, text
    685a30331929add5218e4cae8dcff9fef35e9a0a Thu Jul 31 15:46:11 2025 -0700
    Feedback from code review and hgw0 testing of hubspace. If the hubspace filesystem is mounted, do the replacement in the dataDir string when first setting the dataDir (code review). Later, when stripping the dataDir off the filename to print in the UI, add a check for the mount point so we can correctly strip off the right string from the incoming filename, which will have a different path prefix than on the hbuspace machine.
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    372119b197658e6d7ba8b25a1a6ac653c09e605a Mon Jul 28 10:31:00 2025 -0700
    adding one per user request refs #29545
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    31801be892b78fcf34ef81581e24c33b920c306a Mon Jul 28 15:06:21 2025 -0700
    adding several per user request refs #29545
  • lines changed 74, context: html, text, full: html, text
    79631bad98a7a3a016f29a35ff1fe0e48dbccf11 Fri Aug 1 22:52:14 2025 -0700
    BRC update refs #34337
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
  • lines changed 7, context: html, text, full: html, text
    967d0f8de69dce6f67490147438aec1164015b76 Fri Aug 1 10:48:48 2025 -0700
    make public.hub.txt and hub.txt have the same mtime to avoid duplicate pushing in the otto cron jobs refs #34917
• src/hg/makeDb/doc/asmHubs/runBuild
  • lines changed 166, context: html, text, full: html, text
    d016d8f62aac199e12ae92583784e426b22a1c14 Fri Aug 1 10:38:15 2025 -0700
    catch up to current script with automatic repeat masker identification and email complete message refs #23891
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 69, context: html, text, full: html, text
    79631bad98a7a3a016f29a35ff1fe0e48dbccf11 Fri Aug 1 22:52:14 2025 -0700
    BRC update refs #34337
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    372119b197658e6d7ba8b25a1a6ac653c09e605a Mon Jul 28 10:31:00 2025 -0700
    adding one per user request refs #29545
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 31, context: html, text, full: html, text
    79631bad98a7a3a016f29a35ff1fe0e48dbccf11 Fri Aug 1 22:52:14 2025 -0700
    BRC update refs #34337
• src/hg/makeDb/doc/hg19.gencode.txt
  • lines changed 44, context: html, text, full: html, text
    1a856b5d1ebbb6ff8761c331716af73b3c8aaa1e Tue Jul 29 12:15:26 2025 -0700
    import of GENCODE Versions V49, V49lift37, and VM38
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 44, context: html, text, full: html, text
    1a856b5d1ebbb6ff8761c331716af73b3c8aaa1e Tue Jul 29 12:15:26 2025 -0700
    import of GENCODE Versions V49, V49lift37, and VM38
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    31801be892b78fcf34ef81581e24c33b920c306a Mon Jul 28 15:06:21 2025 -0700
    adding several per user request refs #29545
• src/hg/makeDb/doc/mm39/gencode.txt
  • lines changed 46, context: html, text, full: html, text
    1a856b5d1ebbb6ff8761c331716af73b3c8aaa1e Tue Jul 29 12:15:26 2025 -0700
    import of GENCODE Versions V49, V49lift37, and VM38
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
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    31801be892b78fcf34ef81581e24c33b920c306a Mon Jul 28 15:06:21 2025 -0700
    adding several per user request refs #29545
• src/hg/makeDb/outside/clsLongReadRna/clsTrackTool
  • lines changed 30, context: html, text, full: html, text
    5df12e00d92dfc710671d73ed7bb3a173e2cd789 Mon Aug 4 13:17:44 2025 -0700
    adjustments to clsLongReadRna trackDb to added
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    46849f2053370ff9c0ff9594936d95a51124b162 Mon Aug 4 13:17:44 2025 -0700
    adjustments to clsLongReadRna trackDb to address composite behavior problems
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
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    1a856b5d1ebbb6ff8761c331716af73b3c8aaa1e Tue Jul 29 12:15:26 2025 -0700
    import of GENCODE Versions V49, V49lift37, and VM38
• src/hg/makeDb/outside/hgnc/hgncToBigBed
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    d194838295ec57173a17c36c1552b9aca464cf29 Wed Jul 30 13:18:15 2025 -0700
    fixed HGNC filter; comma+space between allowed values caused very weird breakage
• src/hg/makeDb/outside/hgnc/tests/expected/hg38Test.locus_type.filter.txt
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    d194838295ec57173a17c36c1552b9aca464cf29 Wed Jul 30 13:18:15 2025 -0700
    fixed HGNC filter; comma+space between allowed values caused very weird breakage
• src/hg/makeDb/schema/all.joiner
  • lines changed 277, context: html, text, full: html, text
    1a856b5d1ebbb6ff8761c331716af73b3c8aaa1e Tue Jul 29 12:15:26 2025 -0700
    import of GENCODE Versions V49, V49lift37, and VM38
• src/hg/makeDb/trackDb/human/abSplice.ra
  • lines changed 1, context: html, text, full: html, text
    8e530779a3273d8f34f5932ab98155aee669d8d2 Mon Jul 28 17:57:10 2025 -0700
    Adding the data last updated time on dataVersion for the AbSplice Scores and the SpliceAI tracks, refs #36141
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
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    1a856b5d1ebbb6ff8761c331716af73b3c8aaa1e Tue Jul 29 12:15:26 2025 -0700
    import of GENCODE Versions V49, V49lift37, and VM38
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV49lift37.html
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    1a856b5d1ebbb6ff8761c331716af73b3c8aaa1e Tue Jul 29 12:15:26 2025 -0700
    import of GENCODE Versions V49, V49lift37, and VM38
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV49lift37.ra
  • lines changed 210, context: html, text, full: html, text
    1a856b5d1ebbb6ff8761c331716af73b3c8aaa1e Tue Jul 29 12:15:26 2025 -0700
    import of GENCODE Versions V49, V49lift37, and VM38
• src/hg/makeDb/trackDb/human/hg38/clsLongReadRna.ra
  • lines changed 120, context: html, text, full: html, text
    5df12e00d92dfc710671d73ed7bb3a173e2cd789 Mon Aug 4 13:17:44 2025 -0700
    adjustments to clsLongReadRna trackDb to added
  • lines changed 120, context: html, text, full: html, text
    46849f2053370ff9c0ff9594936d95a51124b162 Mon Aug 4 13:17:44 2025 -0700
    adjustments to clsLongReadRna trackDb to address composite behavior problems
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 2, context: html, text, full: html, text
    fcc66292648958c70053054587910f187ba249d0 Mon Jul 28 15:42:35 2025 -0700
    make setColorWith work a big less weirdly by using an invisible color for the graph when there is nothing in the bigBed.
  • lines changed 3, context: html, text, full: html, text
    ab07ef01b54a3f22034d58444204e02d57eb6c47 Mon Jul 28 16:01:04 2025 -0700
    comment out the setColorWidth to avoid it sneaking out to the RR
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    1a856b5d1ebbb6ff8761c331716af73b3c8aaa1e Tue Jul 29 12:15:26 2025 -0700
    import of GENCODE Versions V49, V49lift37, and VM38
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV48.ra
  • lines changed 1, context: html, text, full: html, text
    1a856b5d1ebbb6ff8761c331716af73b3c8aaa1e Tue Jul 29 12:15:26 2025 -0700
    import of GENCODE Versions V49, V49lift37, and VM38
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV49.html
  • lines changed 47, context: html, text, full: html, text
    1a856b5d1ebbb6ff8761c331716af73b3c8aaa1e Tue Jul 29 12:15:26 2025 -0700
    import of GENCODE Versions V49, V49lift37, and VM38
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV49.ra
  • lines changed 247, context: html, text, full: html, text
    1a856b5d1ebbb6ff8761c331716af73b3c8aaa1e Tue Jul 29 12:15:26 2025 -0700
    import of GENCODE Versions V49, V49lift37, and VM38
• src/hg/makeDb/trackDb/human/panelApp.alpha.ra
  • lines changed 1, context: html, text, full: html, text
    ea9ca019b202a347d3c3e82e64f7834fac3639a9 Thu Jul 31 19:50:23 2025 -0700
    Fixing the 'Link to PanelApp Australia' url on hgc page, refs #35758
• src/hg/makeDb/trackDb/human/spliceAI.ra
  • lines changed 1, context: html, text, full: html, text
    8e530779a3273d8f34f5932ab98155aee669d8d2 Mon Jul 28 17:57:10 2025 -0700
    Adding the data last updated time on dataVersion for the AbSplice Scores and the SpliceAI tracks, refs #36141
• src/hg/makeDb/trackDb/human/trackDb.ra
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    d194838295ec57173a17c36c1552b9aca464cf29 Wed Jul 30 13:18:15 2025 -0700
    fixed HGNC filter; comma+space between allowed values caused very weird breakage
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    45ab96a3f708c02264604a201ec3f0a7c926c7e0 Thu Jul 31 15:26:58 2025 -0700
    Updating the pennantIcon for the PubTator track release, refs #35957
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    14a382607cf9758b4168045c93b6424697e00050 Thu Jul 31 15:31:19 2025 -0700
    Updating the penantIcon for the HGNC update, refs #36073
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    e69a819c8711dd9fe6f8e475e1591ea41516106f Fri Aug 1 13:09:47 2025 -0700
    Announcing the PubTator track for hg38 and hg19, refs #35957
• src/hg/makeDb/trackDb/mouse/mm10/clsLongReadRna.ra
  • lines changed 97, context: html, text, full: html, text
    5df12e00d92dfc710671d73ed7bb3a173e2cd789 Mon Aug 4 13:17:44 2025 -0700
    adjustments to clsLongReadRna trackDb to added
  • lines changed 97, context: html, text, full: html, text
    46849f2053370ff9c0ff9594936d95a51124b162 Mon Aug 4 13:17:44 2025 -0700
    adjustments to clsLongReadRna trackDb to address composite behavior problems
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    1a856b5d1ebbb6ff8761c331716af73b3c8aaa1e Tue Jul 29 12:15:26 2025 -0700
    import of GENCODE Versions V49, V49lift37, and VM38
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM38.html
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    1a856b5d1ebbb6ff8761c331716af73b3c8aaa1e Tue Jul 29 12:15:26 2025 -0700
    import of GENCODE Versions V49, V49lift37, and VM38
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM38.ra
  • lines changed 247, context: html, text, full: html, text
    1a856b5d1ebbb6ff8761c331716af73b3c8aaa1e Tue Jul 29 12:15:26 2025 -0700
    import of GENCODE Versions V49, V49lift37, and VM38
• src/hg/makeDb/trackDb/rhesus/rheMac10/mgap.html
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    1f51934abeb8f1e5aad5915c3323c6d35f0b8d99 Fri Aug 1 15:45:06 2025 -0700
    Fixing broken links to the mGAP website. Making each line less than 100 characters. Adding missing <p> tags. refs #36032
• src/hg/makeDb/trackDb/rhesus/rheMac10/trackDb.ra
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    3822e9e37a2a00edb66773f15f2d0c6a8ee6d750 Fri Aug 1 15:23:16 2025 -0700
    Updating the short and long label. Moving the track from the experimental group to the Variation and repeats, refs #36032
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    ade5f0cc78080686c034c606c6952799a9428ff2 Fri Aug 1 16:38:19 2025 -0700
    Adding a pennantIcon for the mGAP track for rheMac10. No newsarch.html post will be created for this track, refs #36032
• src/hg/utils/automation/doBlastzChainNet.pl
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    c08b66512ffda6f2cf43bd3687a68f710965d08f Thu Jul 31 17:04:18 2025 -0700
    using hgLoadMafSummary.v483 to work around maf dots no redmine
• src/hg/utils/automation/doRecipBest.pl
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    e58683ce4249ec43684a323144f88ca8e56d14a1 Thu Jul 31 17:11:53 2025 -0700
    using hgLoadMafSummary.v483 to work around maf dots no redmine
• src/hg/utils/otto/genArk/devList.sh
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    4fe9ce6537fbfad528c0e2c20e7d6ee36e3729fd Wed Jul 30 15:40:54 2025 -0700
    the cron job that makes the dev.todaylist.gz listing refs #34917
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    ec439df2d702798e3b36edfe7faa47ddafab5521 Wed Jul 30 15:44:28 2025 -0700
    add note about this otto cron job refs #34917
• src/hg/utils/otto/genArk/pushNewOnes.sh
  • lines changed 63, context: html, text, full: html, text
    312be12573fb0c4823e6e30ef5a58e10ae604f8c Wed Jul 30 15:30:07 2025 -0700
    new scripts to replace pushRR.sh and alphaBetaPush.pl for dramatic performance improvement refs #34917
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    cbe6c4ccb2a229070c54d068798b567d3801b604 Thu Jul 31 11:08:32 2025 -0700
    safety check on validity of directory path refs #34917
• src/hg/utils/otto/genArk/pushRR.sh
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    ac52c1b6f5b37ede7efe9748d8cb2a57cab8d2ad Thu Jul 31 11:31:50 2025 -0700
    now running new and improved scripts that are much more efficient refs #34917
• src/hg/utils/otto/genArk/quickPush.pl
  • lines changed 377, context: html, text, full: html, text
    312be12573fb0c4823e6e30ef5a58e10ae604f8c Wed Jul 30 15:30:07 2025 -0700
    new scripts to replace pushRR.sh and alphaBetaPush.pl for dramatic performance improvement refs #34917
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    25232ea095a9222e0c63a940d12557ca6db6122c Wed Jul 30 15:34:46 2025 -0700
    remove the testing grep -v statement refs #34917
• src/hg/utils/otto/otto.crontab
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    5ae22064718499c7c5341f9846e43e56e66a1e21 Wed Jul 30 15:46:28 2025 -0700
    adding the devList.sh script for GenArk pushing reference refs #34917
• src/hg/utils/otto/varChat/varChatOtto.sh
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    34277489b7571b02a541eb567ab88f3383c56ecb Tue Jul 29 12:29:33 2025 -0700
    Fixing a typo in the pipefail line, no Redmine
• src/utils/qa/weeklybld/buildEnv.csh
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    1309381fb01947576684344718daafb15828ff5d Mon Aug 4 13:27:42 2025 -0700
    v486 preview2, refs #36171

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• files changed: 83