All File Changes

v335_base to v336_preview (2016-07-04 to 2016-07-11) v336

• confs/hgwdev.hg.conf
  • lines changed 8, context: html, text, full: html, text
    358a975e2df4b7b95028f2effc6f15b5944d0dd9 Sun Jul 10 01:11:52 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• src/hg/cirm/cdw/cdwChangeAccess/cdwChangeAccess.c
  • lines changed 4, context: html, text, full: html, text
    ca4f189d5ff96544ae97d110590c8a168e8c5ae4 Wed Jun 29 12:57:18 2016 -0700
    Improving usage message.
    
• src/hg/cirm/cdw/cdwGroupFile/cdwGroupFile.c
  • lines changed 4, context: html, text, full: html, text
    711aa7e038188c526492e407cf0afb63c44ffbab Wed Jun 29 12:57:48 2016 -0700
    Improving usage statement.
    
• src/hg/cirm/cdw/cdwMakePairedEndQa/cdwMakePairedEndQa.c
  • lines changed 1, context: html, text, full: html, text
    851f04b27b65e968b4476cf13b87528916237e3e Thu Jul 7 10:02:14 2016 -0700
    Making system look for paired end just within same submission directory.
    
• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 13, context: html, text, full: html, text
    f6807cb2b73ec99113aad8cf086dc5d429d0db40 Thu Jul 7 19:24:55 2016 -0700
    Removing makeReadableTemp and replacing it with calls to cdwReserveTempFile, which now makes readable files as well.
    
• src/hg/cirm/cdw/cdwQaEvaluate/cdwQaEvaluate.c
  • lines changed 1, context: html, text, full: html, text
    851f04b27b65e968b4476cf13b87528916237e3e Thu Jul 7 10:02:14 2016 -0700
    Making system look for paired end just within same submission directory.
    
• src/hg/cirm/cdw/cdwRunDaemon/cdwRunDaemon.c
  • lines changed 1, context: html, text, full: html, text
    d7edb65495f80479330fb733533505cc2a55895f Thu Jul 7 10:02:54 2016 -0700
    Stripping NOSQLINJ out of error message to prevent an error when sticking error message into database.
    
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 39, context: html, text, full: html, text
    f0174240d1c0716a6bbe71bc3be4bdd6517cb57b Wed Jun 29 12:58:55 2016 -0700
    Making it set initial permissions of files based on access metadata tag. Removing life_stage from required fields list.
    
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 1, context: html, text, full: html, text
    851f04b27b65e968b4476cf13b87528916237e3e Thu Jul 7 10:02:14 2016 -0700
    Making system look for paired end just within same submission directory.
    
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 3, context: html, text, full: html, text
    851f04b27b65e968b4476cf13b87528916237e3e Thu Jul 7 10:02:14 2016 -0700
    Making system look for paired end just within same submission directory.
    
  • lines changed 2, context: html, text, full: html, text
    968e50be18fd23411e431708c37a4c2c5f385981 Thu Jul 7 19:23:21 2016 -0700
    Making cdwReserveTempFile make file with our normal permissions.
    
• src/hg/hgGateway/hgGateway.c
  • lines changed 13, context: html, text, full: html, text
    381da604707a65b902707c2f86af896d1a7369e5 Wed Jul 6 15:03:24 2016 -0700
    Adding back support for hg.conf settings survey and surveyLabel to hgGateway.
    
• src/hg/hgGateway/hgGateway.html
  • lines changed 2, context: html, text, full: html, text
    381da604707a65b902707c2f86af896d1a7369e5 Wed Jul 6 15:03:24 2016 -0700
    Adding back support for hg.conf settings survey and surveyLabel to hgGateway.
    
• src/hg/hgMirror/hgMirror
  • lines changed 1, context: html, text, full: html, text
    9cba2cb1cf5c0a2ddb59d8956b6eb735074278a8 Thu Jul 7 14:35:02 2016 -0700
    fixing bug in hg.conf parsing in hgMirror
    
• src/hg/hgPublicSessions/hgPublicSessions.c
  • lines changed 2, context: html, text, full: html, text
    10dd0a10d8475bb6cb01ec2d2e52ad941492c981 Thu Jul 7 15:34:39 2016 -0700
    hgPublicSessions should use the udcCache specified in hg.conf, just like all the other good little CGIs. refs #17659
    
• src/hg/hgSession/hgSession.c
  • lines changed 35, context: html, text, full: html, text
    ae843e42c15f576fcbf9cc4a3671e615cf905a96 Wed Jul 6 12:45:04 2016 -0700
    Additional configuration options for session thumbnail creation and examples for same, refs #17469
    
• src/hg/hgVai/hgVai.c
  • lines changed 21, context: html, text, full: html, text
    64df1dc542e3f7653a5d24cfef8d13d55a22aca2 Thu Jul 7 09:44:07 2016 -0700
    Fixing a couple more places that assume that transcript status tables are in the same database as the gene track. refs #17597
    
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    c4770655923d38c3c11c09c528b6b800b4785269 Mon Jul 11 09:45:53 2016 -0700
    don't use htcGetDnaAliInWindow if you want to show alignments outside
    the window
    
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 3, context: html, text, full: html, text
    758a0c6f1cf2d4bd6c08561d7c375bfc524a0e24 Tue Jul 5 09:47:47 2016 -0700
    Fixing minor typo, refs #17635
    
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 15, context: html, text, full: html, text
    70f6f1e7613aa83917347faaedb9248ae4ee9e85 Thu Jul 7 11:51:05 2016 -0700
    Adding important information about protein query PSL coordinates and sizes.
    
  • lines changed 2, context: html, text, full: html, text
    6b1a9ae6af5fe9a26eb2fbffe15e102630bace29 Thu Jul 7 12:11:55 2016 -0700
    oops, improving the PSL FAQ for prot query
    
• src/hg/htdocs/goldenPath/help/bigMaf.html
  • lines changed 4, context: html, text, full: html, text
    4b556845bbe694dfc50d7bc5e4ac4eca7c25f16e Tue Jul 5 13:56:18 2016 -0700
    Adding a note abou speciesOrder to bigMaf.html refs #15935
    
  • lines changed 1, context: html, text, full: html, text
    bdd2beb83df3dcd0dd3ff27e9d73a376a782fd94 Tue Jul 5 14:41:16 2016 -0700
    Changing example speciesOrder on bigMaf.html to remove hg38 with input from Braney refs #15935
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    6988ae35efa654204fe63b851581fa104d6e846d Thu Jul 7 12:15:14 2016 -0700
    Improving news entry based on code review refs #17632
    
• src/hg/htdocs/indexNews.html
  • lines changed 4, context: html, text, full: html, text
    c51cb812e9c1b1f60e612d99361c43c8d30097e0 Thu Jul 7 14:18:44 2016 -0700
    Made a few mods to template instructions at top of file.
    
• src/hg/js/hgGateway.js
  • lines changed 12, context: html, text, full: html, text
    381da604707a65b902707c2f86af896d1a7369e5 Wed Jul 6 15:03:24 2016 -0700
    Adding back support for hg.conf settings survey and surveyLabel to hgGateway.
    
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    7f3ea3f731bd77129ac9d92bedc27584d8753d20 Wed Jul 6 11:18:53 2016 -0700
    make the list of gene sets in MAF detail page more useful
    
• src/hg/lib/sessionThumbnail.c
  • lines changed 23, context: html, text, full: html, text
    ae843e42c15f576fcbf9cc4a3671e615cf905a96 Wed Jul 6 12:45:04 2016 -0700
    Additional configuration options for session thumbnail creation and examples for same, refs #17469
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 163, context: html, text, full: html, text
    7a4ec9de23ffd2455a3a660989361d9ea04542f1 Wed Jul 6 10:23:34 2016 -0700
    dbSNP b147 (snp147) tracks for hg19 and hg38. refs #17209
    
• src/hg/makeDb/doc/hg38/hg38Patch7.txt
  • lines changed 2, context: html, text, full: html, text
    6eb6bce16a5212ecf5e5a97c10a9144f7886c477 Thu Jul 7 13:55:07 2016 -0700
    finish off download links refs #17134
    
• src/hg/makeDb/doc/hg38/variation.txt
  • lines changed 73, context: html, text, full: html, text
    7a4ec9de23ffd2455a3a660989361d9ea04542f1 Wed Jul 6 10:23:34 2016 -0700
    dbSNP b147 (snp147) tracks for hg19 and hg38. refs #17209
    
• src/hg/makeDb/doc/mm10Patch4/mm10Patch4.txt
  • lines changed 2, context: html, text, full: html, text
    789516292f390ad60d3160c3f801743321833890 Thu Jul 7 13:56:35 2016 -0700
    finish off download links refs #16414
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 19, context: html, text, full: html, text
    7a4ec9de23ffd2455a3a660989361d9ea04542f1 Wed Jul 6 10:23:34 2016 -0700
    dbSNP b147 (snp147) tracks for hg19 and hg38. refs #17209
    
• src/hg/makeDb/trackDb/human/snp147.html
  • lines changed 36, context: html, text, full: html, text
    7a4ec9de23ffd2455a3a660989361d9ea04542f1 Wed Jul 6 10:23:34 2016 -0700
    dbSNP b147 (snp147) tracks for hg19 and hg38. refs #17209
    
• src/hg/makeDb/trackDb/human/snp147.shared.html
  • lines changed 470, context: html, text, full: html, text
    7a4ec9de23ffd2455a3a660989361d9ea04542f1 Wed Jul 6 10:23:34 2016 -0700
    dbSNP b147 (snp147) tracks for hg19 and hg38. refs #17209
    
• src/hg/makeDb/trackDb/human/snp147Common.html
  • lines changed 28, context: html, text, full: html, text
    7a4ec9de23ffd2455a3a660989361d9ea04542f1 Wed Jul 6 10:23:34 2016 -0700
    dbSNP b147 (snp147) tracks for hg19 and hg38. refs #17209
    
• src/hg/makeDb/trackDb/human/snp147Flagged.html
  • lines changed 29, context: html, text, full: html, text
    7a4ec9de23ffd2455a3a660989361d9ea04542f1 Wed Jul 6 10:23:34 2016 -0700
    dbSNP b147 (snp147) tracks for hg19 and hg38. refs #17209
    
• src/hg/makeDb/trackDb/human/snp147Mult.html
  • lines changed 25, context: html, text, full: html, text
    7a4ec9de23ffd2455a3a660989361d9ea04542f1 Wed Jul 6 10:23:34 2016 -0700
    dbSNP b147 (snp147) tracks for hg19 and hg38. refs #17209
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 111, context: html, text, full: html, text
    7a4ec9de23ffd2455a3a660989361d9ea04542f1 Wed Jul 6 10:23:34 2016 -0700
    dbSNP b147 (snp147) tracks for hg19 and hg38. refs #17209
    
• src/hg/makeDb/trackDb/mouse/mm10/genomicSuperDups.html
  • lines changed 1, context: html, text, full: html, text
    3bb8beea4c0452e80f9976fcf2f2e066089aacb2 Wed Jul 6 11:26:29 2016 -0700
    fixing html errors found by hgTablesTest
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 28, context: html, text, full: html, text
    533581c5a612c407be65c5786e3f32d06a998816 Tue Jul 5 16:10:16 2016 -0700
    labels on NCBI RefSeq tracks refs #13673
    
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 628, context: html, text, full: html, text
    88514285206bf0a1fc25f6b94c6690c77ee74255 Mon Jul 11 09:55:34 2016 -0700
    new script to construct assembly hub from NCBI source working on mouse strains refs #13553
    
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 1, context: html, text, full: html, text
    1c31a5719bfc6d4c0ebafb070e95d1ddb8ff4c86 Mon Jun 27 16:53:58 2016 -0700
    Removing unused variable from generated csh script.
    
  • lines changed 2, context: html, text, full: html, text
    584d1e4f4473c9bc9b95d0eed878528698e478a2 Wed Jul 6 10:22:48 2016 -0700
    Oops, don't use hardcoded liftUp file name.
    
• src/hg/utils/automation/doIdKeys.pl
  • lines changed 1, context: html, text, full: html, text
    28958b61488fa6b6bdf2dd39a78b347f07bab383 Tue Jul 5 13:28:07 2016 -0700
    update template with secondsElapsed calculation refs #13553
    
• src/hg/utils/automation/doTemplate.pl
  • lines changed 10, context: html, text, full: html, text
    28958b61488fa6b6bdf2dd39a78b347f07bab383 Tue Jul 5 13:28:07 2016 -0700
    update template with secondsElapsed calculation refs #13553
    
• src/product/ex.hg.conf
  • lines changed 15, context: html, text, full: html, text
    ae843e42c15f576fcbf9cc4a3671e615cf905a96 Wed Jul 6 12:45:04 2016 -0700
    Additional configuration options for session thumbnail creation and examples for same, refs #17469
    
• src/product/installer/README.md
  • lines changed 3, context: html, text, full: html, text
    2ef936ea2b8a6cef2b3e303d2e0abba7706dac2e Tue Jul 5 16:21:46 2016 -0700
    More minor fixups to GBiC README, refs #14399
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    99596cb52ddacd8d8f0f6e3140d3bc19f1699ffd Mon Jul 11 09:58:27 2016 -0700
    v336 preview1 refs #17576
    
• src/utils/qa/weeklybld/doHgTablesTestRobot.csh
  • lines changed 2, context: html, text, full: html, text
    154c80145bb00e9bb7ee03f20845d9ae4e2a734f Mon Jul 4 21:44:26 2016 -0700
    adding qateam email refs #17576
    
  • lines changed 1, context: html, text, full: html, text
    0d781feb32ec2866e265b91e8b4e4ab383a6498a Mon Jul 4 21:48:55 2016 -0700
    correctly browser-qa email refs #17576
    
  • lines changed 1, context: html, text, full: html, text
    ed93a55254a17d4ddbecc6a09b81cae75810e905 Mon Jul 4 21:52:01 2016 -0700
    correctly browser-qa email refs #17576
    
  • lines changed 1, context: html, text, full: html, text
    f374b3cbe77d14ef8bd8f107b649f6530da5b4ec Tue Jul 5 15:07:01 2016 -0700
    oops, do not need 2 ways to do it.
    

• lines changed: 1874
• files changed: 53