All File Changes

v375_preview to v375_preview2 (2018-11-26 to 2018-12-03) v375

• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 2, context: html, text, full: html, text
    624b2c8d70a1c80040b32a447b9137038d072dc0 Mon Dec 3 10:08:26 2018 -0800
    Adding additional subcellular localization values, refs #22551
• src/hg/hgBlat/hgBlat.c
  • lines changed 2, context: html, text, full: html, text
    dd18632fc5902943bb921c3171d867a6e3d7da2b Thu Nov 29 14:24:58 2018 -0800
    adding example seq to hgBlat (no redmine needed as of BrianL)
• src/hg/hgSession/hgSession.c
  • lines changed 5, context: html, text, full: html, text
    d66dce5cf7d97f98254f856374b157c9bd9c7687 Wed Nov 28 09:10:30 2018 -0800
    hgSession prints out short links when an 'hgSession.shortLink' hg.conf variable is on, refs #8520
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 4, context: html, text, full: html, text
    32d4ec45f05fdc1b8634a225ac50c8724b6e41d5 Fri Nov 30 13:37:07 2018 -0800
    missing a closing semi colon ; on an nbsp tag no redmine
• src/hg/hgTracks/lollipop.c
  • lines changed 34, context: html, text, full: html, text
    2d81b4d18b40cd67b0a96d15ea2cd88adc2bbfab Wed Nov 28 13:54:00 2018 -0800
    changing genbank to not use /scratch/data
• src/hg/hgc/gencodeClick.c
  • lines changed 34, context: html, text, full: html, text
    f9d47d16a47f128366aeb1deb0575c0cb52aa0f9 Thu Nov 29 15:24:08 2018 -0800
    For native GENCODE on GRCh37/hg19, link to http://grch37.ensembl.org, not primary GENCODE site. #22549
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 15, context: html, text, full: html, text
    4ee39edaeeb5d95ffce283cdf4c978e73a60b752 Mon Nov 26 13:29:10 2018 -0800
    Adding FAQ entry for TB output file order #21790
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 6, context: html, text, full: html, text
    594ca30bc51bdfa69bba1ed1de1cf4b6efef0a23 Thu Nov 29 15:33:09 2018 -0800
    switching order of ponAbe assembly release on credits.html, refs #22521
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 12, context: html, text, full: html, text
    f73d78913c7d1a67ad7d9e9f49543beaddba6355 Mon Nov 26 14:55:33 2018 -0800
    Adding IP addresses to the Assembly hub Quick Start Page
  • lines changed 4, context: html, text, full: html, text
    7d6220183105c20a6f2fb489bd49d30e787bb21c Mon Nov 26 16:37:28 2018 -0800
    Adding a link to our Public Hub IP list on an Asssembly Hub page note33 refs #17700
  • lines changed 4, context: html, text, full: html, text
    b0267b27fb89ddb20ef10e238da0008ff8db39db Mon Nov 26 16:44:04 2018 -0800
    cleaning up a paragraph tag ref #17700
• src/hg/htdocs/goldenPath/help/wiggle.html
  • lines changed 3, context: html, text, full: html, text
    b790a71f34ebb268c8dd3b03e5c1065963254e91 Fri Nov 30 08:43:59 2018 -0800
    Clarifying that wig format does not support NaN ref#22535
• src/hg/htdocs/images/phylo/dm6_124way.png
  • lines changed 0, context: html, text, full: html, text
    5c099d22c8723ee83f05fe97d9897266960afa2e Tue Nov 27 09:59:30 2018 -0800
    better organization of the tree refs #18874
  • lines changed 0, context: html, text, full: html, text
    0d1eddfd96c689220bde25f45a534899fb9e8a79 Sun Dec 2 20:36:25 2018 -0800
    better organization for Drosophila refs #22550
• src/hg/htdocs/indexNews.html
  • lines changed 1, context: html, text, full: html, text
    2c60732dfc6f4e9d11727fab85b93d9213aa8f0a Tue Nov 27 08:22:19 2018 -0800
    Fixing chicken link anchor
• src/hg/inc/lollipop.h
  • lines changed 0, context: html, text, full: html, text
    2d81b4d18b40cd67b0a96d15ea2cd88adc2bbfab Wed Nov 28 13:54:00 2018 -0800
    changing genbank to not use /scratch/data
• src/hg/lib/bigLolly.as
  • lines changed 14, context: html, text, full: html, text
    2d81b4d18b40cd67b0a96d15ea2cd88adc2bbfab Wed Nov 28 13:54:00 2018 -0800
    changing genbank to not use /scratch/data
  • lines changed 14, context: html, text, full: html, text
    cac1441bfc2875dfc102efd2f69fee5f79a11f47 Sun Dec 2 08:29:04 2018 -0800
    remove bigLolly.as for the moment
• src/hg/makeDb/doc/cotJap2/initialBuild.txt
  • lines changed 365, context: html, text, full: html, text
    157ae7b6fc196366a112335d1711301b55f8dd80 Mon Nov 26 11:19:01 2018 -0800
    QA Ready refs #22330
• src/hg/makeDb/doc/dm6/multiz124way.txt
  • lines changed 634, context: html, text, full: html, text
    b939070d9eafdd9d916c86dd68748f94c14738f7 Tue Nov 27 10:18:31 2018 -0800
    completed 4d tree estimation refs #18874
  • lines changed 236, context: html, text, full: html, text
    52717264a14fc9f930ec580215f1433069dede6c Fri Nov 30 13:44:44 2018 -0800
    QA ready refs #22550
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 165, context: html, text, full: html, text
    cc34104c13dd702c0ffe6a472cc0b01b6a428b87 Mon Nov 26 11:00:34 2018 -0800
    finish off cotJap2 lastz/chainNet and bosTau9 on hg38 refs #22330
• src/hg/makeDb/doc/mm10.txt
  • lines changed 8, context: html, text, full: html, text
    cc34104c13dd702c0ffe6a472cc0b01b6a428b87 Mon Nov 26 11:00:34 2018 -0800
    finish off cotJap2 lastz/chainNet and bosTau9 on hg38 refs #22330
  • lines changed 116, context: html, text, full: html, text
    06bdfd182de8188305ff771d920969db22ec468e Fri Nov 30 11:45:33 2018 -0800
    import of GECODE VM20 prerelease
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 2, context: html, text, full: html, text
    3af217e6360ee7a9e27798ae2dc769bae8c518d0 Wed Nov 28 11:50:57 2018 -0800
    use the correct haplotype mapping for hg19 and hg38
  • lines changed 384, context: html, text, full: html, text
    2d81b4d18b40cd67b0a96d15ea2cd88adc2bbfab Wed Nov 28 13:54:00 2018 -0800
    changing genbank to not use /scratch/data
• src/hg/makeDb/genbank/src/align/gbAlignSetup
  • lines changed 1, context: html, text, full: html, text
    2d81b4d18b40cd67b0a96d15ea2cd88adc2bbfab Wed Nov 28 13:54:00 2018 -0800
    changing genbank to not use /scratch/data
• src/hg/makeDb/genbank/src/gbConf/gbConf.c
  • lines changed 1, context: html, text, full: html, text
    2d81b4d18b40cd67b0a96d15ea2cd88adc2bbfab Wed Nov 28 13:54:00 2018 -0800
    changing genbank to not use /scratch/data
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 6, context: html, text, full: html, text
    06bdfd182de8188305ff771d920969db22ec468e Fri Nov 30 11:45:33 2018 -0800
    import of GECODE VM20 prerelease
• src/hg/makeDb/trackDb/birds/cotJap2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    c28e944f96d346bd8b1f1895fad7fc77e77c884e Mon Nov 26 10:28:15 2018 -0800
    adding crispr 10K track refs #22330
• src/hg/makeDb/trackDb/cat/felCat3/multiz4way.html
  • lines changed 4, context: html, text, full: html, text
    22f089f89445ea4cd757fbb82eb909ff5d18769f Fri Nov 30 09:07:26 2018 -0800
    Updating http to https for felCat3, uiLinks cronjob.
• src/hg/makeDb/trackDb/cat/felCat3/phastConsElements4way.html
  • lines changed 5, context: html, text, full: html, text
    22f089f89445ea4cd757fbb82eb909ff5d18769f Fri Nov 30 09:07:26 2018 -0800
    Updating http to https for felCat3, uiLinks cronjob.
• src/hg/makeDb/trackDb/cat/felCat3/xenoRefGene.html
  • lines changed 1, context: html, text, full: html, text
    22f089f89445ea4cd757fbb82eb909ff5d18769f Fri Nov 30 09:07:26 2018 -0800
    Updating http to https for felCat3, uiLinks cronjob.
• src/hg/makeDb/trackDb/chicken/galGal6/chainNetBirds.ra
  • lines changed 21, context: html, text, full: html, text
    02a232e0d2292009a824295de5547f4f457c369d Mon Nov 26 10:18:39 2018 -0800
    adding cotJap2 chainNet lastz definitions refs #22330
• src/hg/makeDb/trackDb/drosophila/dm6/chainNetInsects.html
  • lines changed 172, context: html, text, full: html, text
    6c41a21bcb9ee787fda0ece49b20b02c8aec79d7 Fri Nov 30 13:41:14 2018 -0800
    adding html description page refs #22550
• src/hg/makeDb/trackDb/drosophila/dm6/chainNetInsects.ra
  • lines changed 55, context: html, text, full: html, text
    a04ef5a8563e40327e5885553ecd91b17ea56052 Thu Nov 29 11:41:59 2018 -0800
    proper ordering of tracks in the Comparative Genomics section refs #18874
  • lines changed 1, context: html, text, full: html, text
    5e97ba62ad1412cf711b5dd2370abd5ba2ba175c Fri Nov 30 10:20:28 2018 -0800
    change group flies to holometabola refs #22550
  • lines changed 2, context: html, text, full: html, text
    6c41a21bcb9ee787fda0ece49b20b02c8aec79d7 Fri Nov 30 13:41:14 2018 -0800
    adding html description page refs #22550
• src/hg/makeDb/trackDb/drosophila/dm6/cons124way.html
  • lines changed 1051, context: html, text, full: html, text
    48b318233ab209b7a19ebe275f0cb3e068d77e62 Wed Nov 28 19:00:39 2018 -0800
    adding description page refs #18874
• src/hg/makeDb/trackDb/drosophila/dm6/trackDb.124way.ra
  • lines changed 4, context: html, text, full: html, text
    a04ef5a8563e40327e5885553ecd91b17ea56052 Thu Nov 29 11:41:59 2018 -0800
    proper ordering of tracks in the Comparative Genomics section refs #18874
  • lines changed 4, context: html, text, full: html, text
    36d8ba58967f7379a38ff3e6d78efa7152563dbe Fri Nov 30 11:13:37 2018 -0800
    set track labels to 124 insects instead of species refs #22550
  • lines changed 6, context: html, text, full: html, text
    612cccf76af0e88abd0fbe9e302e0afcc2138985 Fri Nov 30 12:59:28 2018 -0800
    eliminate the unnecessary subGroup2 clade selections refs #22550
• src/hg/makeDb/trackDb/drosophila/dm6/trackDb.124wayMafNet.ra
  • lines changed 1, context: html, text, full: html, text
    e564fce61a54e3611d8335ac9d7d4ed71dc89aa9 Tue Nov 27 11:15:16 2018 -0800
    visibility hide refs #18874
  • lines changed 5, context: html, text, full: html, text
    a04ef5a8563e40327e5885553ecd91b17ea56052 Thu Nov 29 11:41:59 2018 -0800
    proper ordering of tracks in the Comparative Genomics section refs #18874
• src/hg/makeDb/trackDb/drosophila/dm6/trackDb.124wayRbest.ra
  • lines changed 1, context: html, text, full: html, text
    e564fce61a54e3611d8335ac9d7d4ed71dc89aa9 Tue Nov 27 11:15:16 2018 -0800
    visibility hide refs #18874
  • lines changed 1, context: html, text, full: html, text
    a04ef5a8563e40327e5885553ecd91b17ea56052 Thu Nov 29 11:41:59 2018 -0800
    proper ordering of tracks in the Comparative Genomics section refs #18874
• src/hg/makeDb/trackDb/drosophila/dm6/trackDb.124waySyn.ra
  • lines changed 1, context: html, text, full: html, text
    e564fce61a54e3611d8335ac9d7d4ed71dc89aa9 Tue Nov 27 11:15:16 2018 -0800
    visibility hide refs #18874
  • lines changed 1, context: html, text, full: html, text
    a04ef5a8563e40327e5885553ecd91b17ea56052 Thu Nov 29 11:41:59 2018 -0800
    proper ordering of tracks in the Comparative Genomics section refs #18874
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    93d216748e3e906fe0ac67ba7620c1c70fecfc82 Fri Nov 30 10:42:25 2018 -0800
    set specific ensGene outlink to their special grch37 site refs #22539
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    f022dcce207f95d4f720a21a69eda574b39976c5 Tue Nov 27 16:01:28 2018 -0800
    Removed release tags for the miRNA track following CGI release
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    f741c74a4847a3a495659437ea5052c13d6d7d1c Mon Nov 26 14:11:40 2018 -0800
    Removing the maxWindowToDraw limitation for the snp151Mult track, refs #21010
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    06bdfd182de8188305ff771d920969db22ec468e Fri Nov 30 11:45:33 2018 -0800
    import of GECODE VM20 prerelease
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM20.html
  • lines changed 30, context: html, text, full: html, text
    06bdfd182de8188305ff771d920969db22ec468e Fri Nov 30 11:45:33 2018 -0800
    import of GECODE VM20 prerelease
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM20.ra
  • lines changed 286, context: html, text, full: html, text
    06bdfd182de8188305ff771d920969db22ec468e Fri Nov 30 11:45:33 2018 -0800
    import of GECODE VM20 prerelease
• src/hg/makeDb/trackDb/refSeqComposite.html
  • lines changed 3, context: html, text, full: html, text
    b1ee3add8d2d18fc3b7ac33838bca958ff325720 Tue Nov 27 13:04:50 2018 -0800
    updating refSeqComposite.html, not all assemblies have diff tracks, refs #22499
• src/hg/makeDb/trackDb/sgpGene.html
  • lines changed 3, context: html, text, full: html, text
    22f089f89445ea4cd757fbb82eb909ff5d18769f Fri Nov 30 09:07:26 2018 -0800
    Updating http to https for felCat3, uiLinks cronjob.
• src/hg/makeDb/trackDb/trackDb.chainNet.birds.ra
  • lines changed 54, context: html, text, full: html, text
    02a232e0d2292009a824295de5547f4f457c369d Mon Nov 26 10:18:39 2018 -0800
    adding cotJap2 chainNet lastz definitions refs #22330
• src/hg/utils/automation/doSameSpeciesLiftOver.pl
  • lines changed 4, context: html, text, full: html, text
    77ab001ecb4937b1a842a1089b521265651e81e0 Thu Nov 29 10:48:20 2018 -0800
    clarify target if fromDb and query is toDb refs #22546
• src/hg/utils/phyloTrees/binaryTree.pl
  • lines changed 1, context: html, text, full: html, text
    2c63b54a1f782f28122bab6cf7fc76f2edbad065 Wed Nov 28 09:47:12 2018 -0800
    print distance even when -noInternal refs #22113
• src/product/installer/browserSetup.sh
  • lines changed 2, context: html, text, full: html, text
    ffee0217681e44d7f66b527c21b20f736631a87b Thu Nov 29 08:03:30 2018 -0800
    fixing GBIC problem on Amazon AWS reported by Li Qingqin
  • lines changed 14, context: html, text, full: html, text
    855a1fc43a3c32ce812717d5503172e082455d3f Mon Dec 3 05:44:58 2018 -0800
    trying to avoid error abort on Selinux disabling in gbic, refs #22555
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    7a6b5cb455c18a83028a3140c4e02bc3651f1c6f Mon Dec 3 10:16:10 2018 -0800
    v375 preview2, refs #22531

• lines changed: 3818
• files changed: 62