All File Changes

v454_preview2 to v454_base (2023-09-11 to 2023-09-18) v454

• confs/hgwbeta.hg.conf
  • lines changed 1, context: html, text, full: html, text
    1c2c9a70dcf5b00514cb41ebf499b0c5ebbf4e4b Sun Sep 17 01:11:19 2023 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 1, context: html, text, full: html, text
    1c2c9a70dcf5b00514cb41ebf499b0c5ebbf4e4b Sun Sep 17 01:11:19 2023 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 1, context: html, text, full: html, text
    1c2c9a70dcf5b00514cb41ebf499b0c5ebbf4e4b Sun Sep 17 01:11:19 2023 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgGene/wikiTrack.c
  • lines changed 3, context: html, text, full: html, text
    d04faff33041e920ec52024866efc52314d60787 Fri Sep 15 16:32:12 2023 -0700
    updating these last hgGene wiki links, Hiram says much of it is obsolete now anyways.
  • lines changed 3, context: html, text, full: html, text
    3ab184ad97bdfee9fe5cc318a07f6bc2704f04e1 Fri Sep 15 17:54:26 2023 -0700
    Revert "updating these last hgGene wiki links, Hiram says much of it is obsolete now anyways." This reverts commit d04faff33041e920ec52024866efc52314d60787.
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 1, context: html, text, full: html, text
    15fd95da3778b7c1c3a8fcacb8e2f1da57c3e66e Thu Sep 14 09:06:31 2023 -0700
    Tiny tweak to capitalization change on new hgHubConnect link. Refs #32047
• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 16, context: html, text, full: html, text
    b6d356738ffdf5562cc71d22bacbfa1f0c5c65c4 Tue Sep 12 16:16:04 2023 -0700
    Add linkout (per subtree) to MicrobeTrace (in addition to Nextstrain) if subtreeSize is at most 500.
  • lines changed 8, context: html, text, full: html, text
    a6288fe651a8fa52b1510ee6c6b7ecb9db00dcd6 Thu Sep 14 10:02:50 2023 -0700
    Added description of MicrobeTrace to 'More information' section.
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 120, context: html, text, full: html, text
    b6d356738ffdf5562cc71d22bacbfa1f0c5c65c4 Tue Sep 12 16:16:04 2023 -0700
    Add linkout (per subtree) to MicrobeTrace (in addition to Nextstrain) if subtreeSize is at most 500.
  • lines changed 1, context: html, text, full: html, text
    b0db90c8f3e14751e17423f7e48ce6700468d61a Fri Sep 15 08:30:30 2023 -0700
    Fix typo in Nextstrain subtree link from result tables. HT @FedeGueli
  • lines changed 44, context: html, text, full: html, text
    8032b3fdf26b7de0f295588f47265207c0e41520 Fri Sep 15 10:40:41 2023 -0700
    Include MicrobeTrace subtree links in results table.
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 5, context: html, text, full: html, text
    b6d356738ffdf5562cc71d22bacbfa1f0c5c65c4 Tue Sep 12 16:16:04 2023 -0700
    Add linkout (per subtree) to MicrobeTrace (in addition to Nextstrain) if subtreeSize is at most 500.
  • lines changed 2, context: html, text, full: html, text
    8032b3fdf26b7de0f295588f47265207c0e41520 Fri Sep 15 10:40:41 2023 -0700
    Include MicrobeTrace subtree links in results table.
• src/hg/hgTables/galaxy.c
  • lines changed 1, context: html, text, full: html, text
    cb8c0b5aec5b78aa6693d1df261752fd3f1a6ca5 Fri Sep 15 12:21:42 2023 -0700
    Fixing hgTables for redirect-to-https. Galaxy will now work correctly since we give it our URL in a vaiable of that name, now updated in galaxy.c and mainPage.c. Fixed a few minor URLs to documentation too.
  • lines changed 1, context: html, text, full: html, text
    389da7069662a418d17f77728ad454c6bc34955b Fri Sep 15 17:55:58 2023 -0700
    Revert "Fixing hgTables for redirect-to-https. Galaxy will now work correctly since we give it our URL in a vaiable of that name, now updated in galaxy.c and mainPage.c. Fixed a few minor URLs to documentation too." This reverts commit cb8c0b5aec5b78aa6693d1df261752fd3f1a6ca5.
• src/hg/hgTables/great.c
  • lines changed 1, context: html, text, full: html, text
    cb8c0b5aec5b78aa6693d1df261752fd3f1a6ca5 Fri Sep 15 12:21:42 2023 -0700
    Fixing hgTables for redirect-to-https. Galaxy will now work correctly since we give it our URL in a vaiable of that name, now updated in galaxy.c and mainPage.c. Fixed a few minor URLs to documentation too.
  • lines changed 1, context: html, text, full: html, text
    389da7069662a418d17f77728ad454c6bc34955b Fri Sep 15 17:55:58 2023 -0700
    Revert "Fixing hgTables for redirect-to-https. Galaxy will now work correctly since we give it our URL in a vaiable of that name, now updated in galaxy.c and mainPage.c. Fixed a few minor URLs to documentation too." This reverts commit cb8c0b5aec5b78aa6693d1df261752fd3f1a6ca5.
• src/hg/hgTables/hgTables.c
  • lines changed 1, context: html, text, full: html, text
    cb8c0b5aec5b78aa6693d1df261752fd3f1a6ca5 Fri Sep 15 12:21:42 2023 -0700
    Fixing hgTables for redirect-to-https. Galaxy will now work correctly since we give it our URL in a vaiable of that name, now updated in galaxy.c and mainPage.c. Fixed a few minor URLs to documentation too.
  • lines changed 1, context: html, text, full: html, text
    389da7069662a418d17f77728ad454c6bc34955b Fri Sep 15 17:55:58 2023 -0700
    Revert "Fixing hgTables for redirect-to-https. Galaxy will now work correctly since we give it our URL in a vaiable of that name, now updated in galaxy.c and mainPage.c. Fixed a few minor URLs to documentation too." This reverts commit cb8c0b5aec5b78aa6693d1df261752fd3f1a6ca5.
• src/hg/hgTables/mainPage.c
  • lines changed 1, context: html, text, full: html, text
    cb8c0b5aec5b78aa6693d1df261752fd3f1a6ca5 Fri Sep 15 12:21:42 2023 -0700
    Fixing hgTables for redirect-to-https. Galaxy will now work correctly since we give it our URL in a vaiable of that name, now updated in galaxy.c and mainPage.c. Fixed a few minor URLs to documentation too.
  • lines changed 1, context: html, text, full: html, text
    389da7069662a418d17f77728ad454c6bc34955b Fri Sep 15 17:55:58 2023 -0700
    Revert "Fixing hgTables for redirect-to-https. Galaxy will now work correctly since we give it our URL in a vaiable of that name, now updated in galaxy.c and mainPage.c. Fixed a few minor URLs to documentation too." This reverts commit cb8c0b5aec5b78aa6693d1df261752fd3f1a6ca5.
• src/hg/hgTables/schema.c
  • lines changed 1, context: html, text, full: html, text
    cb8c0b5aec5b78aa6693d1df261752fd3f1a6ca5 Fri Sep 15 12:21:42 2023 -0700
    Fixing hgTables for redirect-to-https. Galaxy will now work correctly since we give it our URL in a vaiable of that name, now updated in galaxy.c and mainPage.c. Fixed a few minor URLs to documentation too.
  • lines changed 1, context: html, text, full: html, text
    389da7069662a418d17f77728ad454c6bc34955b Fri Sep 15 17:55:58 2023 -0700
    Revert "Fixing hgTables for redirect-to-https. Galaxy will now work correctly since we give it our URL in a vaiable of that name, now updated in galaxy.c and mainPage.c. Fixed a few minor URLs to documentation too." This reverts commit cb8c0b5aec5b78aa6693d1df261752fd3f1a6ca5.
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    4d0ec03bf50216ce33794e39f638c27c7baa1fa1 Fri Sep 15 13:36:43 2023 -0700
    Fixing up hgTracks URLs for redirect to https.
  • lines changed 2, context: html, text, full: html, text
    a04a741ac3f31b7b10b30c38fa088b9405d2c1e9 Fri Sep 15 17:54:54 2023 -0700
    Revert "Fixing up hgTracks URLs for redirect to https." This reverts commit 4d0ec03bf50216ce33794e39f638c27c7baa1fa1.
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    7ce75d997ca3a25acea7dd48b5f0c4473c50b0b2 Fri Sep 15 13:21:42 2023 -0700
    minor fix in parsing authors, add https too.
  • lines changed 2, context: html, text, full: html, text
    de178594aa7a5480496a75575e48b7412ba57d59 Fri Sep 15 17:55:03 2023 -0700
    Revert "minor fix in parsing authors, add https too." This reverts commit 7ce75d997ca3a25acea7dd48b5f0c4473c50b0b2.
• src/hg/hgc/wikiTrack.c
  • lines changed 2, context: html, text, full: html, text
    dae18b453735298b725e40f0a457856849f1b38f Fri Sep 15 13:01:58 2023 -0700
    updating hgc URLs for https redirect. wiki system had two updates.
  • lines changed 2, context: html, text, full: html, text
    818dfe5553f0e279f17bf5ffb86ad10dc2da1b8e Fri Sep 15 17:55:31 2023 -0700
    Revert "updating hgc URLs for https redirect. wiki system had two updates." This reverts commit dae18b453735298b725e40f0a457856849f1b38f.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 24, context: html, text, full: html, text
    6299b299a5d53c9fc50f1080c47da08c458899e8 Fri Sep 15 15:48:55 2023 -0700
    Announcing the new COSMIC track for hg38, refs #29625
  • lines changed 1, context: html, text, full: html, text
    0574f108e4b4cf66bc8f72e6043c7b56bc8799db Fri Sep 15 15:57:27 2023 -0700
    FIxing the COSMIC Regions track link, refs #29625
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    6299b299a5d53c9fc50f1080c47da08c458899e8 Fri Sep 15 15:48:55 2023 -0700
    Announcing the new COSMIC track for hg38, refs #29625
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    aebb39bf84fcc61c71d9c044557d143676913d90 Mon Sep 18 12:16:04 2023 -0700
    New version number v454
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    05d1f709f575f899f165d40c76d669acc7c070b9 Fri Sep 15 10:05:51 2023 -0700
    Make mathWigs not downloadable in current region because they are not supported in the api yet, refs #21342
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 7, context: html, text, full: html, text
    a6567f587ac2ec91253d6a6b8218b7813ac18d8a Thu Sep 14 08:29:31 2023 -0700
    adding 7 primates per user request refs #29545
  • lines changed 5, context: html, text, full: html, text
    dccf7e0790249aa078f928342b68552d583bc0a1 Sat Sep 16 20:01:17 2023 -0700
    adding two bacteria per user request refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    dccf7e0790249aa078f928342b68552d583bc0a1 Sat Sep 16 20:01:17 2023 -0700
    adding two bacteria per user request refs #29545
• src/hg/makeDb/doc/evaSnp5.txt
  • lines changed 1, context: html, text, full: html, text
    c874d12e8680a17fffa2d6d6f4d64a66c1a3878c Mon Sep 11 16:57:10 2023 -0700
    Fixing a spot where I forgot to change 4 to 5, feedback from CR refs #32223
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 59, context: html, text, full: html, text
    abbf180d9e199d5aed519621da3dd67cbfce6a8b Mon Sep 11 23:27:18 2023 -0700
    adding 55 for an update refs @29545
  • lines changed 1, context: html, text, full: html, text
    1aac3751f8b66c9923eaeb249a59b6614881cf32 Tue Sep 12 23:05:58 2023 -0700
    remove an illegal name conflict refs #29545
• src/hg/makeDb/doc/hg38/hprc90way.txt
  • lines changed 185, context: html, text, full: html, text
    1b4517a48758b5adac8797e0d390d99ab7de7c53 Wed Sep 13 11:04:11 2023 -0700
    adding VCF tracks refs #3156`
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 27, context: html, text, full: html, text
    1ef2a104da75e45c173ea0b04fcbb944634481e8 Mon Sep 11 17:41:14 2023 -0700
    adding 20 for an update refs #29545
• src/hg/makeDb/doc/mm10.txt
  • lines changed 24, context: html, text, full: html, text
    eb6de8ad5a6634621b0d522debabc0cad84a8051 Mon Sep 11 15:32:03 2023 -0700
    adding allGaps track per user request refs #32104
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 23, context: html, text, full: html, text
    fd8e3a17dd49cee7e073bbda64b77a15067c08e2 Mon Sep 11 16:21:08 2023 -0700
    adding 11 for an update refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 7, context: html, text, full: html, text
    a6567f587ac2ec91253d6a6b8218b7813ac18d8a Thu Sep 14 08:29:31 2023 -0700
    adding 7 primates per user request refs #29545
• src/hg/makeDb/trackDb/human/hg38/cosmicMuts.html
  • lines changed 3, context: html, text, full: html, text
    f3c36b712d07474f88c7b58925c6c600c63aca54 Tue Sep 12 13:14:01 2023 -0700
    Updating the identifier and ID labels, refs #29625
• src/hg/makeDb/trackDb/human/hg38/hprcArr.ra
  • lines changed 2, context: html, text, full: html, text
    c17429328984b7bd3a1e2316d7a00b10084e993c Wed Sep 13 11:15:19 2023 -0700
    slightly change long label in HPRC inversions track
• src/hg/makeDb/trackDb/human/hg38/hprcVCF.ra
  • lines changed 37, context: html, text, full: html, text
    2a151c9c5064f5b98c8a4eea08ef1d298ef94651 Wed Sep 13 10:58:01 2023 -0700
    add over 3 and under 4 size VCF tracks and is now a supertrack refs #31561
• src/hg/makeDb/trackDb/human/hg38/mane.html
  • lines changed 8, context: html, text, full: html, text
    1a0b94702e72f4f1a0e64d7ade491dc05278a194 Thu Sep 14 12:24:53 2023 -0700
    Adding new MANE otto job, refs #32237
• src/hg/makeDb/trackDb/human/hg38/mane.ra
  • lines changed 6, context: html, text, full: html, text
    1a0b94702e72f4f1a0e64d7ade491dc05278a194 Thu Sep 14 12:24:53 2023 -0700
    Adding new MANE otto job, refs #32237
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    6299b299a5d53c9fc50f1080c47da08c458899e8 Fri Sep 15 15:48:55 2023 -0700
    Announcing the new COSMIC track for hg38, refs #29625
• src/hg/makeDb/trackDb/mouse/mm10/allGaps.html
  • lines changed 31, context: html, text, full: html, text
    e31d9c193494dac9988c8949b7b78980271e4091 Mon Sep 11 15:23:33 2023 -0700
    add allGaps track per user request refs #32104
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    e31d9c193494dac9988c8949b7b78980271e4091 Mon Sep 11 15:23:33 2023 -0700
    add allGaps track per user request refs #32104
• src/hg/perf/hgTracksRandom.c
  • lines changed 1, context: html, text, full: html, text
    a18c62ec699f6dea35ed25995cf28c40f0650480 Wed Sep 13 08:58:27 2023 -0700
    Increasing the load time required for hgTracksRandom to complain from 5s to 10s. This is because genome-asia routinely takes 6-8s to load. Also, this cron does not monitor speed, it is an alert system for when a mirror/comp is down entirely or reacting very slowly. It still serves this same purpose with the 10s time, just fewer emails for the team. Refs email 9/11/2023 to browser-alert group.
• src/hg/utils/otto/genCC/doGenCC.py
  • lines changed 254, context: html, text, full: html, text
    d3601e38c97b27789949531a71b5c0fe54db5454 Thu Sep 14 15:02:16 2023 -0700
    Updating GenCC .as file, updating data, and making it an otto track. Refs #31795
• src/hg/utils/otto/mane/doMane.py
  • lines changed 44, context: html, text, full: html, text
    1a0b94702e72f4f1a0e64d7ade491dc05278a194 Thu Sep 14 12:24:53 2023 -0700
    Adding new MANE otto job, refs #32237
• src/hg/utils/otto/otto.crontab
  • lines changed 3, context: html, text, full: html, text
    1a0b94702e72f4f1a0e64d7ade491dc05278a194 Thu Sep 14 12:24:53 2023 -0700
    Adding new MANE otto job, refs #32237
  • lines changed 3, context: html, text, full: html, text
    d3601e38c97b27789949531a71b5c0fe54db5454 Thu Sep 14 15:02:16 2023 -0700
    Updating GenCC .as file, updating data, and making it an otto track. Refs #31795
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 58, context: html, text, full: html, text
    5f5a688287ed55e160046b1d2dabfb3117092fc2 Tue Sep 5 11:59:19 2023 -0700
    Added BA.2_*_27945 labels for homoplasic C27945T (unfortunately also designated as BA.2.65 which is more like a mini-BA.2) to avoid pangolin-data flip-flops of BA.2/BA.2.65 from one release to the next. Removed BA.5.2.1_no28330 label since its branch is gone after some permanent-exclusion cleanup. Added a bunch of new lineages.
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    aebb39bf84fcc61c71d9c044557d143676913d90 Mon Sep 18 12:16:04 2023 -0700
    New version number v454
• src/utils/qa/hubSearchUpdate
  • lines changed 13, context: html, text, full: html, text
    467eb80b7e23879950955aa41284b69e0dc9f159 Thu Sep 14 16:19:01 2023 -0700
    Add track hub trix indexes to hubSearchText otto update, refs #30253
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    a6f743036300a1ea0325a1484545f2bcc99907d6 Mon Sep 18 12:14:01 2023 -0700
    v454 final build, refs #32203

• lines changed: 1087
• files changed: 62