All File Changes

v461_preview2 to v461_base (2024-02-12 to 2024-02-19) v461

• src/hg/cirm/cdw/lib/cdwPageHeader.h
  • lines changed 2, context: html, text, full: html, text
    c01d6c197c915f6e08993ed670981232c2fced3a Tue Feb 13 10:08:30 2024 -0800
    fixing header links agian, per parisa
• src/hg/cirm/gateway/htdocs/cirmIndex.html
  • lines changed 142, context: html, text, full: html, text
    62ecd77e45bd8f2944233a1bd185512b0734607c Tue Feb 13 10:03:05 2024 -0800
    cirm page rename as per parisa
• src/hg/cirm/gateway/htdocs/inc/header.html
  • lines changed 2, context: html, text, full: html, text
    4b6cbebdabff06b38a4cc814bf8fb941eac913fa Tue Feb 13 10:05:31 2024 -0800
    fixing cirm header links, per parisa
• src/hg/cirm/gateway/htdocs/sspsygene.html
  • lines changed 142, context: html, text, full: html, text
    62ecd77e45bd8f2944233a1bd185512b0734607c Tue Feb 13 10:03:05 2024 -0800
    cirm page rename as per parisa
• src/hg/hgTables/mainPage.c
  • lines changed 15, context: html, text, full: html, text
    93504f18ac014caf2aa30b03c8d6c710fecbd2d2 Tue Feb 13 17:55:26 2024 -0800
    When a hub composite track is selected in the table browser, show the shortlabel of the subtracks in the table dropdown in addition to the subtrack name, since the track name may not be informative, as in the case of the ENCODE DNA track hub, refs 33000
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 1, context: html, text, full: html, text
    c7c1525e8eba2c94300290fd4c7806dea60df954 Tue Feb 13 10:49:34 2024 -0800
    don't expect to find a bigDataUrl in a composite header
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 45, context: html, text, full: html, text
    63656c54eadd4f059fd7ac184c57f53d2081db29 Tue Feb 13 14:09:51 2024 -0800
    Announcing the release of All GENCODE for hg38, hg19 (V45), and mm39 (VM34). refs #32411 #32413 #32412
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    63656c54eadd4f059fd7ac184c57f53d2081db29 Tue Feb 13 14:09:51 2024 -0800
    Announcing the release of All GENCODE for hg38, hg19 (V45), and mm39 (VM34). refs #32411 #32413 #32412
• src/hg/inc/hui.h
  • lines changed 1, context: html, text, full: html, text
    f3c7b669da695e4919410f08f0a3f6fa21778796 Thu Feb 15 15:13:10 2024 -0800
    get hgTrackUi to do the right thing if "type bigBed" is specified.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    731e70a56c0bba9a52531926aef6321b3fd4c48e Mon Feb 19 10:41:12 2024 -0800
    New version number v461
• src/hg/lib/bigDbSnp.c
  • lines changed 1, context: html, text, full: html, text
    7256393cc0ec2ff7f9a2c3322c69ccf39b99e4db Fri Feb 9 09:51:55 2024 -0800
    dbsnp label change, refs #32901
• src/hg/lib/hui.c
  • lines changed 3, context: html, text, full: html, text
    f3c7b669da695e4919410f08f0a3f6fa21778796 Thu Feb 15 15:13:10 2024 -0800
    get hgTrackUi to do the right thing if "type bigBed" is specified.
• src/hg/lib/trackDbCustom.c
  • lines changed 9, context: html, text, full: html, text
    f3c7b669da695e4919410f08f0a3f6fa21778796 Thu Feb 15 15:13:10 2024 -0800
    get hgTrackUi to do the right thing if "type bigBed" is specified.
  • lines changed 1, context: html, text, full: html, text
    a9d11dd882c0f5cc95f2257e09c379df18067e3b Thu Feb 15 15:16:24 2024 -0800
    oops, some drek got accidentally checked in
• src/hg/makeDb/doc/asmHubs/chromAuthority.pl
  • lines changed 10, context: html, text, full: html, text
    e3daa44c78dbe581a4cc1fbdaf071aee36c0e46d Fri Feb 16 10:09:11 2024 -0800
    allow a manual override of chromAuthority refs #29545
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    fd2b6400802b1b13718080dcef09d10bec1947bd Tue Feb 13 13:01:01 2024 -0800
    adding a couple of assemblies per user request refs #29545
  • lines changed 1, context: html, text, full: html, text
    5ff5206aee0c9a1b57bc6e8443ec820de0189ad6 Fri Feb 16 09:41:02 2024 -0800
    adding a second Plasmodium to catch up with PlasmoDb refs #29545
  • lines changed 40, context: html, text, full: html, text
    176447e76f5e9b9a9b37b6e3954587fc4e3cb1c4 Sat Feb 17 22:41:29 2024 -0800
    an update to catch up VGP assemblies refs #29545
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
  • lines changed 4, context: html, text, full: html, text
    919d6e358931333184e22114fa8fe85e204a8a25 Wed Feb 14 15:08:36 2024 -0800
    also sending out the repeatModeler .stk.gz and .out.gz files no redmine
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 9, context: html, text, full: html, text
    176447e76f5e9b9a9b37b6e3954587fc4e3cb1c4 Sat Feb 17 22:41:29 2024 -0800
    an update to catch up VGP assemblies refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 8, context: html, text, full: html, text
    176447e76f5e9b9a9b37b6e3954587fc4e3cb1c4 Sat Feb 17 22:41:29 2024 -0800
    an update to catch up VGP assemblies refs #29545
• src/hg/makeDb/doc/hg38/gnomad.txt
  • lines changed 7, context: html, text, full: html, text
    190f783626730bf88e10253b6f763f72a4bb190a Fri Feb 16 11:48:28 2024 -0800
    Staging gnomAD v3.1.1 non-cancer filter track, refs #32916
• src/hg/makeDb/doc/hg38/hprcQuickLift.txt
  • lines changed 35, context: html, text, full: html, text
    7fda78a4052001b31148cdc2167dfc6dae8b0eee Tue Feb 13 10:54:38 2024 -0800
    starting again on quickLift
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    5ff5206aee0c9a1b57bc6e8443ec820de0189ad6 Fri Feb 16 09:41:02 2024 -0800
    adding a second Plasmodium to catch up with PlasmoDb refs #29545
  • lines changed 2, context: html, text, full: html, text
    176447e76f5e9b9a9b37b6e3954587fc4e3cb1c4 Sat Feb 17 22:41:29 2024 -0800
    an update to catch up VGP assemblies refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 4, context: html, text, full: html, text
    176447e76f5e9b9a9b37b6e3954587fc4e3cb1c4 Sat Feb 17 22:41:29 2024 -0800
    an update to catch up VGP assemblies refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    176447e76f5e9b9a9b37b6e3954587fc4e3cb1c4 Sat Feb 17 22:41:29 2024 -0800
    an update to catch up VGP assemblies refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 13, context: html, text, full: html, text
    176447e76f5e9b9a9b37b6e3954587fc4e3cb1c4 Sat Feb 17 22:41:29 2024 -0800
    an update to catch up VGP assemblies refs #29545
  • lines changed 1, context: html, text, full: html, text
    ac1b89d4efca259844a53e2335769c1fd26b2e79 Mon Feb 19 09:20:31 2024 -0800
    GRCr8 does not exist as a GenArk hub refs #29545
• src/hg/makeDb/doc/mm39/chrM.ncbiRefSeq.txt
  • lines changed 108, context: html, text, full: html, text
    d78f2f29016298f39d54b536b0b51a9ff8ffbff9 Mon Feb 12 15:07:39 2024 -0800
    procedure to add selective annotations to ncbiRefSeq tables refs #32902
• src/hg/makeDb/doc/mm39/gffToLink.pl
  • lines changed 113, context: html, text, full: html, text
    d78f2f29016298f39d54b536b0b51a9ff8ffbff9 Mon Feb 12 15:07:39 2024 -0800
    procedure to add selective annotations to ncbiRefSeq tables refs #32902
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    fd2b6400802b1b13718080dcef09d10bec1947bd Tue Feb 13 13:01:01 2024 -0800
    adding a couple of assemblies per user request refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    fd2b6400802b1b13718080dcef09d10bec1947bd Tue Feb 13 13:01:01 2024 -0800
    adding a couple of assemblies per user request refs #29545
  • lines changed 9, context: html, text, full: html, text
    176447e76f5e9b9a9b37b6e3954587fc4e3cb1c4 Sat Feb 17 22:41:29 2024 -0800
    an update to catch up VGP assemblies refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    17fcb215cc545daac98634782459e189e6a696a1 Tue Feb 13 13:02:39 2024 -0800
    update a couple of assemblies refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    17fcb215cc545daac98634782459e189e6a696a1 Tue Feb 13 13:02:39 2024 -0800
    update a couple of assemblies refs #29545
• src/hg/makeDb/trackDb/human/hg19/prs.ra
  • lines changed 2, context: html, text, full: html, text
    b108137cb511a53842fc2b20e9b22780a11abee2 Thu Feb 15 17:27:30 2024 -0800
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    63656c54eadd4f059fd7ac184c57f53d2081db29 Tue Feb 13 14:09:51 2024 -0800
    Announcing the release of All GENCODE for hg38, hg19 (V45), and mm39 (VM34). refs #32411 #32413 #32412
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    b108137cb511a53842fc2b20e9b22780a11abee2 Thu Feb 15 17:27:30 2024 -0800
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV44lift37.ra
  • lines changed 1, context: html, text, full: html, text
    4220eddde0da8416dc1ec636e43fb00590e1afe1 Tue Feb 13 12:09:46 2024 -0800
    Staging 3 All GENCODE tracks, refs #32411 #32413 #32412
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV45lift37.ra
  • lines changed 1, context: html, text, full: html, text
    4220eddde0da8416dc1ec636e43fb00590e1afe1 Tue Feb 13 12:09:46 2024 -0800
    Staging 3 All GENCODE tracks, refs #32411 #32413 #32412
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 35, context: html, text, full: html, text
    190f783626730bf88e10253b6f763f72a4bb190a Fri Feb 16 11:48:28 2024 -0800
    Staging gnomAD v3.1.1 non-cancer filter track, refs #32916
  • lines changed 1, context: html, text, full: html, text
    98ba5855c2b16d7e34697ade37d496ea4eace33d Fri Feb 16 11:50:00 2024 -0800
    Add release tag to work in progress gnomAD 3.1.1 non-cancer track
• src/hg/makeDb/trackDb/human/hg38/trackDb.470way.ra
  • lines changed 5, context: html, text, full: html, text
    dfc35a15894e59bd06fe94e53b97f6a23393b53c Wed Feb 14 09:40:34 2024 -0800
    Re-adding the tags to this track which I removed in order to hide the overall track when the files were missing from hgdownload.
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    63656c54eadd4f059fd7ac184c57f53d2081db29 Tue Feb 13 14:09:51 2024 -0800
    Announcing the release of All GENCODE for hg38, hg19 (V45), and mm39 (VM34). refs #32411 #32413 #32412
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    ad7f8eb8720a5c6abc92ee1306696fcea610a9f7 Mon Feb 12 15:32:05 2024 -0800
    Reenabling the cactus tracks now that the files have been uploaded to hgwdownload2. No RM.
  • lines changed 1, context: html, text, full: html, text
    b108137cb511a53842fc2b20e9b22780a11abee2 Thu Feb 15 17:27:30 2024 -0800
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV44.ra
  • lines changed 1, context: html, text, full: html, text
    4220eddde0da8416dc1ec636e43fb00590e1afe1 Tue Feb 13 12:09:46 2024 -0800
    Staging 3 All GENCODE tracks, refs #32411 #32413 #32412
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV45.ra
  • lines changed 1, context: html, text, full: html, text
    4220eddde0da8416dc1ec636e43fb00590e1afe1 Tue Feb 13 12:09:46 2024 -0800
    Staging 3 All GENCODE tracks, refs #32411 #32413 #32412
• src/hg/makeDb/trackDb/human/hs1/hoffmanMappability.ra
  • lines changed 1, context: html, text, full: html, text
    b108137cb511a53842fc2b20e9b22780a11abee2 Thu Feb 15 17:27:30 2024 -0800
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    b108137cb511a53842fc2b20e9b22780a11abee2 Thu Feb 15 17:27:30 2024 -0800
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    63656c54eadd4f059fd7ac184c57f53d2081db29 Tue Feb 13 14:09:51 2024 -0800
    Announcing the release of All GENCODE for hg38, hg19 (V45), and mm39 (VM34). refs #32411 #32413 #32412
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    b108137cb511a53842fc2b20e9b22780a11abee2 Thu Feb 15 17:27:30 2024 -0800
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM33.ra
  • lines changed 1, context: html, text, full: html, text
    4220eddde0da8416dc1ec636e43fb00590e1afe1 Tue Feb 13 12:09:46 2024 -0800
    Staging 3 All GENCODE tracks, refs #32411 #32413 #32412
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM34.ra
  • lines changed 1, context: html, text, full: html, text
    4220eddde0da8416dc1ec636e43fb00590e1afe1 Tue Feb 13 12:09:46 2024 -0800
    Staging 3 All GENCODE tracks, refs #32411 #32413 #32412
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    b108137cb511a53842fc2b20e9b22780a11abee2 Thu Feb 15 17:27:30 2024 -0800
    Squashing old pennantIcons.
• src/inc/common.mk
  • lines changed 61, context: html, text, full: html, text
    ae6f7e1ca5938410ff8189423ddc9f365f5a0804 Tue Feb 13 03:38:37 2024 -0800
    The common.mk file is getting hard to read in part because the parts that are run on hgwdev are not obvious to see, they're hidden under five layers of "if" statements. So I'm starting to move everything that is only run on hgwdev into a separate section, at the end as an override. Email from cluster-admin, telling us the libpng is not statically linked anymore. No redmine.
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    731e70a56c0bba9a52531926aef6321b3fd4c48e Mon Feb 19 10:41:12 2024 -0800
    New version number v461
• src/product/installer/browserSetup.sh
  • lines changed 3, context: html, text, full: html, text
    efd23e0e990180e1a6275e416bf6e94e3c53c929 Fri Feb 9 07:46:33 2024 -0800
    fixing bug in browserSetup.sh script, reported by user, refs #32988
• src/utils/hubMake/hubMake
  • lines changed 355, context: html, text, full: html, text
    7ff1a8946d6fb9871fd5b0f0786b0c223406cc01 Wed Feb 14 11:12:29 2024 -0800
    first shot at a hubMake tool, no redmine yet
• src/utils/hubMake/makefile
  • lines changed 14, context: html, text, full: html, text
    7ff1a8946d6fb9871fd5b0f0786b0c223406cc01 Wed Feb 14 11:12:29 2024 -0800
    first shot at a hubMake tool, no redmine yet
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    8247b7f379142552a87ac8a354a4ead37dd4e6ab Mon Feb 19 10:38:10 2024 -0800
    v461 final build, refs #32981

• lines changed: 1253
• files changed: 62