All File Changes

v425_base to v426_preview (2022-01-10 to 2022-01-18) v426

• confs/hgwbeta.hg.conf
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    3d7c4b51c367ac9d7bfc582a00617f300eb4ecde Sun Jan 16 01:11:39 2022 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 27, context: html, text, full: html, text
    e97a753159896bb15164878212d470fbaff926d5 Thu Jan 13 10:28:31 2022 -0800
    Removing incognito mode refs #28520
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    5d0b587678811913bc8609d1a986cd8ef267f013 Thu Jan 13 10:30:15 2022 -0800
    Removing incognito mode doc refs #28520
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 8, context: html, text, full: html, text
    9add99453760c10170441f9ac73add6f17126b62 Tue Jan 11 17:03:51 2022 -0800
    Officially archiving the 2021 news, and adding new 2022 tag. No RM
• src/hg/htdocs/inc/recTrackSets.hg19.tab
  • lines changed 1, context: html, text, full: html, text
    d78141b96e8575777cf07baf350c865a7c15daed Tue Jan 11 16:47:30 2022 -0800
    Removing the dash from the non-coding RTS link, which, while still displaying the data in the RTS properly, the label at the top right of hgTracks would not appear. refs #28707
• src/hg/makeDb/doc/asmHubs/lastzRuns.txt
  • lines changed 105, context: html, text, full: html, text
    8d6e4bf13ec2765165ac377b74c8f904fd672cb0 Tue Jan 18 10:04:37 2022 -0800
    dog GCF_014441545.1 vs. Dog CanFam3 lastz/chain/net run for user, refs #28757
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 7, context: html, text, full: html, text
    464c85c118a4b9d1ec6479cf0f36bca8f9574081 Tue Jan 11 09:15:08 2022 -0800
    adding two per user request refs #28689
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    8e3bea319a5a9fd3f5614c3384395094bb92159d Tue Jan 11 09:24:43 2022 -0800
    adding two assemblies per user request refs #28689
• src/hg/makeDb/doc/hg19.gencode.txt
  • lines changed 46, context: html, text, full: html, text
    a7d5080da217a1cc9ab8006cc34ccac66b4dbcff Sun Jan 16 14:54:57 2022 -0800
    import of GENCODE 39lift37'
• src/hg/makeDb/doc/hg19.txt
  • lines changed 8, context: html, text, full: html, text
    a4d9358b20d4aac8c28a45b8b083ddaa01d8642e Thu Jan 13 10:42:29 2022 -0800
    MakeDoc commits for jaspar 2022 refs #28322
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 35, context: html, text, full: html, text
    f235b09ced2d435593280279b20c4f5c38f9d64e Sat Jan 15 21:21:24 2022 -0800
    import final release of GENCODE V39
• src/hg/makeDb/doc/hg38/jaspar.txt
  • lines changed 9, context: html, text, full: html, text
    a4d9358b20d4aac8c28a45b8b083ddaa01d8642e Thu Jan 13 10:42:29 2022 -0800
    MakeDoc commits for jaspar 2022 refs #28322
• src/hg/makeDb/doc/mm10.txt
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    a4d9358b20d4aac8c28a45b8b083ddaa01d8642e Thu Jan 13 10:42:29 2022 -0800
    MakeDoc commits for jaspar 2022 refs #28322
• src/hg/makeDb/doc/mm39/gencode.txt
  • lines changed 37, context: html, text, full: html, text
    0f37d4d1e887a759881ddfb77210df9cf6c3acdb Sun Jan 16 13:53:12 2022 -0800
    inport of All GENCODE VM28
• src/hg/makeDb/doc/mm39/jaspar.txt
  • lines changed 9, context: html, text, full: html, text
    a4d9358b20d4aac8c28a45b8b083ddaa01d8642e Thu Jan 13 10:42:29 2022 -0800
    MakeDoc commits for jaspar 2022 refs #28322
• src/hg/makeDb/doc/rn5.txt
  • lines changed 103, context: html, text, full: html, text
    5578389fb6a724225e9c67b28ead1712a3745ee5 Mon Jan 10 15:00:46 2022 -0800
    rn5 vs. rn7 lastz/chain/net run for user, refs #28726
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    8e3bea319a5a9fd3f5614c3384395094bb92159d Tue Jan 11 09:24:43 2022 -0800
    adding two assemblies per user request refs #28689
• src/hg/makeDb/doc/wuhCor1/primers.txt
  • lines changed 13, context: html, text, full: html, text
    166150aa69d0368b0722303ff60a178e480c09a2 Mon Jan 10 20:15:26 2022 -0800
    Adding ARTIC v4.1 (fixes some primers for Omicron).
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 2, context: html, text, full: html, text
    f235b09ced2d435593280279b20c4f5c38f9d64e Sat Jan 15 21:21:24 2022 -0800
    import final release of GENCODE V39
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    0f37d4d1e887a759881ddfb77210df9cf6c3acdb Sun Jan 16 13:53:12 2022 -0800
    inport of All GENCODE VM28
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    a7d5080da217a1cc9ab8006cc34ccac66b4dbcff Sun Jan 16 14:54:57 2022 -0800
    import of GENCODE 39lift37'
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    a7d5080da217a1cc9ab8006cc34ccac66b4dbcff Sun Jan 16 14:54:57 2022 -0800
    import of GENCODE 39lift37'
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    f235b09ced2d435593280279b20c4f5c38f9d64e Sat Jan 15 21:21:24 2022 -0800
    import final release of GENCODE V39
• src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
  • lines changed 4, context: html, text, full: html, text
    4654fecc7b9d5d905365bd72fee9d3fa4cb6724f Thu Jan 13 12:38:46 2022 -0800
    Staging updates to clingen tracks: slightly rework the otto job after changes to the clinGen website, get out links on description pages correct, refs #28453
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    0f37d4d1e887a759881ddfb77210df9cf6c3acdb Sun Jan 16 13:53:12 2022 -0800
    inport of All GENCODE VM28
• src/hg/makeDb/trackDb/virus/wuhCor1/articV4_1.html
  • lines changed 42, context: html, text, full: html, text
    120181e612c2107e31aac13bcfa3288b7cc4ef7c Tue Jan 11 13:26:53 2022 -0800
    Adding ARTIC v4.1 (fixes some primers for Omicron).
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    166150aa69d0368b0722303ff60a178e480c09a2 Mon Jan 10 20:15:26 2022 -0800
    Adding ARTIC v4.1 (fixes some primers for Omicron).
• src/hg/utils/otto/clinGen/clinGenCnv.as
  • lines changed 30, context: html, text, full: html, text
    4654fecc7b9d5d905365bd72fee9d3fa4cb6724f Thu Jan 13 12:38:46 2022 -0800
    Staging updates to clingen tracks: slightly rework the otto job after changes to the clinGen website, get out links on description pages correct, refs #28453
• src/hg/utils/otto/clinGen/clinGenDosageHaplo.as
  • lines changed 4, context: html, text, full: html, text
    4654fecc7b9d5d905365bd72fee9d3fa4cb6724f Thu Jan 13 12:38:46 2022 -0800
    Staging updates to clingen tracks: slightly rework the otto job after changes to the clinGen website, get out links on description pages correct, refs #28453
• src/hg/utils/otto/clinGen/clinGenDosageTriplo.as
  • lines changed 4, context: html, text, full: html, text
    4654fecc7b9d5d905365bd72fee9d3fa4cb6724f Thu Jan 13 12:38:46 2022 -0800
    Staging updates to clingen tracks: slightly rework the otto job after changes to the clinGen website, get out links on description pages correct, refs #28453
• src/hg/utils/otto/clinGen/makeDosage.sh
  • lines changed 43, context: html, text, full: html, text
    4654fecc7b9d5d905365bd72fee9d3fa4cb6724f Thu Jan 13 12:38:46 2022 -0800
    Staging updates to clingen tracks: slightly rework the otto job after changes to the clinGen website, get out links on description pages correct, refs #28453
• src/hg/utils/otto/clinGen/makeGeneValidity.sh
  • lines changed 24, context: html, text, full: html, text
    4654fecc7b9d5d905365bd72fee9d3fa4cb6724f Thu Jan 13 12:38:46 2022 -0800
    Staging updates to clingen tracks: slightly rework the otto job after changes to the clinGen website, get out links on description pages correct, refs #28453
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    ac27d7813d12d6ab32beb763204e6fb4dc8ad538 Tue Jan 18 10:21:48 2022 -0800
    Fix path bug in clinGen gene-disease validity build script, refs Lou email
• src/hg/utils/otto/clinGen/makefile
  • lines changed 17, context: html, text, full: html, text
    4654fecc7b9d5d905365bd72fee9d3fa4cb6724f Thu Jan 13 12:38:46 2022 -0800
    Staging updates to clingen tracks: slightly rework the otto job after changes to the clinGen website, get out links on description pages correct, refs #28453
• src/hg/utils/otto/clinGen/processClinGenDosage.py
  • lines changed 46, context: html, text, full: html, text
    4654fecc7b9d5d905365bd72fee9d3fa4cb6724f Thu Jan 13 12:38:46 2022 -0800
    Staging updates to clingen tracks: slightly rework the otto job after changes to the clinGen website, get out links on description pages correct, refs #28453
• src/hg/utils/otto/orphanet/checkOrphanet.sh
  • lines changed 2, context: html, text, full: html, text
    0a5b7d4334d05788314f2c5dd001257fbc774c3b Tue Jan 11 16:21:03 2022 -0800
    Adding the global flag for robustness, needed if orphanet ever goes over 1M items. refs #28686
• src/utils/qa/assemblyStatsCron.py
  • lines changed 112, context: html, text, full: html, text
    20e3ee6ed0d5dd9ef3e54f64bac6e802002e8eb2 Fri Jan 14 09:26:50 2022 -0800
    Adding logic to check for genome-asia hubs, cleaning up the hubStatus logic so that public hubs never sneak into the list, and combining the report and save cronjobs into a single cron. No RM.
• src/utils/qa/assemblyStatsCronSaveStats.py
  • lines changed 214, context: html, text, full: html, text
    20e3ee6ed0d5dd9ef3e54f64bac6e802002e8eb2 Fri Jan 14 09:26:50 2022 -0800
    Adding logic to check for genome-asia hubs, cleaning up the hubStatus logic so that public hubs never sneak into the list, and combining the report and save cronjobs into a single cron. No RM.
• src/utils/qa/checkHTTPS
  • lines changed 1, context: html, text, full: html, text
    264a2adf9f451fa97fc754aa8aef2993d948cda6 Tue Jan 11 06:55:11 2022 -0800
    Removing api site from checked certs since it is not owned by us, no RM
• src/utils/qa/makefile
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    f13e4a602cbdf7ca250f7b77c128a4641f3b18e1 Fri Jan 14 09:29:58 2022 -0800
    Removing the saveStats script since its funtionality was added to the original script assemblyStatsCron.
• src/utils/qa/weeklybld/buildEnv.csh
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    6aa6029b9075e8f3ae9fc12b1ba548d0e93c918d Tue Jan 18 10:28:10 2022 -0800
    v426 preview1, refs #28762

• lines changed: 1006
• files changed: 41