All File Changes

v300_preview2 to v300_base (2014-05-12 to 2014-05-19) v300

• src/browserbox/README.txt
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    removed my symlinks as they tend to confuse everyone, including myself
• src/browserbox/usr/local/apache/htdocs/folders
  • lines changed 1, context: html, text, full: html, text
    removed my symlinks as they tend to confuse everyone, including myself
• src/browserbox/usr/local/apache/trash
  • lines changed 1, context: html, text, full: html, text
    removed my symlinks as they tend to confuse everyone, including myself
• src/browserbox/usr/local/apache/userdata
  • lines changed 1, context: html, text, full: html, text
    removed my symlinks as they tend to confuse everyone, including myself
• src/browserbox/var/lib/mysql
  • lines changed 1, context: html, text, full: html, text
    removed my symlinks as they tend to confuse everyone, including myself
• src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c
  • lines changed 2, context: html, text, full: html, text
    Consistent sort order for replicates. Refs Stanford #1372
  • lines changed 14, context: html, text, full: html, text
    1. Show EDW submission on browse page while uploading. 2. Minor layout changes for readability. refs Stanford #1372
  • lines changed 4, context: html, text, full: html, text
    1. Switch to new URL for encodedcc site. 2. Restore 'No files submitted' message (found by QA). 3. Remove now-superflous message about start time. refs Stanford #1372
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 4, context: html, text, full: html, text
    Drop the sentence "or someone you know who already does have an "ENCODE Data Warehouse account, and have them create an account for you with
    http://%s/cgi-bin/edwWebCreateUser" error message from edwWebSubmit when
    a non-existent user tries to submit a validated.txt.
    
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
  • lines changed 6, context: html, text, full: html, text
    Using edwAddQaEnrichTarget add introns, exons, and promoter regionsas enrichment targets for dm3 (flyBasegene) and ce10 (ensGene)
    
• src/hg/hgGene/domains.c
  • lines changed 1, context: html, text, full: html, text
    update hgGene to use new SCOP URL format
• src/hg/hgGene/geneReviews.c
  • lines changed 1, context: html, text, full: html, text
    When display geneReviews related article on refGene and UCSC gene detail page,Associated the NBKid link to gr-short name only, for example, for SOD1, display
    
    GeneReviews article(s) related to gene SOD1:
    als-overview (Amyotrophic Lateral Sclerosis Overview)
    /|\ /|\
    | |
    NBKid link No Link
    
• src/hg/hgGene/hgGeneData/C_elegans/ce6/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    some tweaks to hg38/knownGene.html and making hg38 the default assemblyfor blastTabs on mm10, rn4, dm3, ce6, sacCer3
    
• src/hg/hgGene/hgGeneData/D_melanogaster/dm3/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    some tweaks to hg38/knownGene.html and making hg38 the default assemblyfor blastTabs on mm10, rn4, dm3, ce6, sacCer3
    
• src/hg/hgGene/hgGeneData/Mouse/mm10/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    some tweaks to hg38/knownGene.html and making hg38 the default assemblyfor blastTabs on mm10, rn4, dm3, ce6, sacCer3
    
• src/hg/hgGene/hgGeneData/Rat/rn4/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    some tweaks to hg38/knownGene.html and making hg38 the default assemblyfor blastTabs on mm10, rn4, dm3, ce6, sacCer3
    
• src/hg/hgGene/hgGeneData/S_cerevisiae/sacCer3/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    some tweaks to hg38/knownGene.html and making hg38 the default assemblyfor blastTabs on mm10, rn4, dm3, ce6, sacCer3
    
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 96, context: html, text, full: html, text
    adding the ability to search hubs for content.
• src/hg/hgLogin/makefile
  • lines changed 2, context: html, text, full: html, text
    Don't override HG_WARN that is set in inc/common.mk .
• src/hg/hgMirror/makefile
  • lines changed 2, context: html, text, full: html, text
    fixing makefile after feedback from Hiram
  • lines changed 2, context: html, text, full: html, text
    fixing makefile after feedback from Braney
• src/hg/hgTracks/cds.c
  • lines changed 4, context: html, text, full: html, text
    Mac OS X Mavericks gcc -Wall complained about the parentheses in this "if"condition split up by #ifdef/#else/#endif. Fix: simplify the syntax so the
    "if" condition is not split.
    
• src/hg/hgc/geneReviewsClick.c
  • lines changed 2, context: html, text, full: html, text
    When display geneReviews related article on refGene and UCSC gene detail page,Associated the NBKid link to gr-short name only, for example, for SOD1, display
    
    GeneReviews article(s) related to gene SOD1:
    als-overview (Amyotrophic Lateral Sclerosis Overview)
    /|\ /|\
    | |
    NBKid link No Link
    
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    fix bug with crashing hgc pages #13262
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 35, context: html, text, full: html, text
    added news announcement for hg38 ucsc genes release
• src/hg/htdocs/indexNews.html
  • lines changed 78, context: html, text, full: html, text
    added news announcement for hg38 ucsc genes release
• src/hg/htdocs/style/encode3Ucsc.css
  • lines changed 4, context: html, text, full: html, text
    1. Show EDW submission on browse page while uploading. 2. Minor layout changes for readability. refs Stanford #1372
• src/hg/inc/hubConnect.h
  • lines changed 2, context: html, text, full: html, text
    adding the ability to search hubs for content.
• src/hg/inc/trackHub.h
  • lines changed 2, context: html, text, full: html, text
    adding the ability to search hubs for content.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v300
• src/hg/js/edwPersona.js
  • lines changed 1, context: html, text, full: html, text
    jshinted
• src/hg/js/encodeDataSummary.js
  • lines changed 3, context: html, text, full: html, text
    jshint doesn't like global variables used in iterators. refs #13255
• src/hg/lib/bacEndPairs.sql
  • lines changed 1, context: html, text, full: html, text
    hg38 has longer chrom names for the bacEnds track sql file
• src/hg/lib/cart.c
  • lines changed 8, context: html, text, full: html, text
    Mac OS X Mavericks gcc -Wall detects unused INLINE functions;getting rid of the one it found.
    
• src/hg/lib/hubPublic.as
  • lines changed 1, context: html, text, full: html, text
    adding the ability to search hubs for content.
• src/hg/lib/hubPublic.sql
  • lines changed 1, context: html, text, full: html, text
    adding the ability to search hubs for content.
• src/hg/lib/hui.c
  • lines changed 15, context: html, text, full: html, text
    fix pennantIcon code to reflect the documentation.
• src/hg/lib/trackHub.c
  • lines changed 19, context: html, text, full: html, text
    adding the ability to search hubs for content.
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes15.csh
  • lines changed 5, context: html, text, full: html, text
    add knownToHprd
  • lines changed 8, context: html, text, full: html, text
    load Vidal, Wanker, and P2P gene sorter tables
• src/hg/makeDb/trackDb/apis/apiMel2/brhInparalog.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on bee (apiMel2) description page
• src/hg/makeDb/trackDb/apis/apiMel2/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on bee (apiMel2) description page
• src/hg/makeDb/trackDb/apis/apiMel2/gold.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on bee (apiMel2) description page
• src/hg/makeDb/trackDb/apis/apiMel2/modelRefGene.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on bee (apiMel2) description page
• src/hg/makeDb/trackDb/blastHg17KG.html
  • lines changed 6, context: html, text, full: html, text
    Changes to opossum (monDom1) description pages
• src/hg/makeDb/trackDb/drosophila/dm3/description.html
  • lines changed 3, context: html, text, full: html, text
    Removing broken link, noted by user, refs #13272
• src/hg/makeDb/trackDb/human/hg38/knownGene.html
  • lines changed 3, context: html, text, full: html, text
    a few tweaks to the hg38 knownGene page
  • lines changed 6, context: html, text, full: html, text
    remove CCDS from text
  • lines changed 8, context: html, text, full: html, text
    some tweaks to hg38/knownGene.html and making hg38 the default assemblyfor blastTabs on mm10, rn4, dm3, ce6, sacCer3
    
• src/hg/makeDb/trackDb/mostConserved.html
  • lines changed 35, context: html, text, full: html, text
    Changes to opossum (monDom1) description pages
• src/hg/makeDb/trackDb/opossum/monDom1/description.html
  • lines changed 1, context: html, text, full: html, text
    Changes to opossum (monDom1) description pages
• src/hg/makeDb/trackDb/opossum/multiz5way.html
  • lines changed 38, context: html, text, full: html, text
    Changes to opossum (monDom1) description pages
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    skunk project
• src/hg/near/hgNear/hgNearData/Human/acc.html
  • lines changed 2, context: html, text, full: html, text
    clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
    for Wanker, Vidal, and P2P.
    
• src/hg/near/hgNear/hgNearData/Human/columnDb.ra
  • lines changed 27, context: html, text, full: html, text
    clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
    for Wanker, Vidal, and P2P.
    
• src/hg/near/hgNear/hgNearData/Human/hg17/columnDb.ra
  • lines changed 28, context: html, text, full: html, text
    clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
    for Wanker, Vidal, and P2P.
    
• src/hg/near/hgNear/hgNearData/Human/hg17/orderDb.ra
  • lines changed 19, context: html, text, full: html, text
    clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
    for Wanker, Vidal, and P2P.
    
• src/hg/near/hgNear/hgNearData/Human/hg18/acc.html
  • lines changed 2, context: html, text, full: html, text
    clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
    for Wanker, Vidal, and P2P.
    
• src/hg/near/hgNear/hgNearData/Human/hg18/columnDb.ra
  • lines changed 28, context: html, text, full: html, text
    clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
    for Wanker, Vidal, and P2P.
    
• src/hg/near/hgNear/hgNearData/Human/hg18/orderDb.ra
  • lines changed 19, context: html, text, full: html, text
    clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
    for Wanker, Vidal, and P2P.
    
• src/hg/near/hgNear/hgNearData/Human/hg19/acc.html
  • lines changed 2, context: html, text, full: html, text
    clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
    for Wanker, Vidal, and P2P.
    
• src/hg/near/hgNear/hgNearData/Human/hg19/columnDb.ra
  • lines changed 27, context: html, text, full: html, text
    clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
    for Wanker, Vidal, and P2P.
    
• src/hg/near/hgNear/hgNearData/Human/hg19/orderDb.ra
  • lines changed 19, context: html, text, full: html, text
    clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
    for Wanker, Vidal, and P2P.
    
• src/hg/near/hgNear/hgNearData/Human/orderDb.ra
  • lines changed 19, context: html, text, full: html, text
    clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
    for Wanker, Vidal, and P2P.
    
• src/hg/utils/hubPublicCheck/hubPublicCheck.c
  • lines changed 14, context: html, text, full: html, text
    adding the ability to search hubs for content.
  • lines changed 4, context: html, text, full: html, text
    Mac OS X Mavericks gcc -Wall found a use of uninitialized variablethat had been missed by earlier versions, probably because the
    uninitialized variable was never used. Got rid of the unused variable.
    
• src/hg/utils/otto/geneReviews/buildGeneReviews.sh
  • lines changed 70, context: html, text, full: html, text
    Feature #5522geneReviews track automatic update
    
  • lines changed 3, context: html, text, full: html, text
    Track #13281 GeneReviews for hg38Add hg38 to the otto geneReviews party
    
• src/hg/utils/otto/geneReviews/checkGeneReviews.sh
  • lines changed 55, context: html, text, full: html, text
    Feature #5522geneReviews track automatic update
    
  • lines changed 2, context: html, text, full: html, text
    Track #13281 GeneReviews for hg38Add hg38 to the otto geneReviews party
    
• src/hg/utils/otto/geneReviews/geneReviews.tables
  • lines changed 2, context: html, text, full: html, text
    Feature #5522geneReviews track automatic update
    
• src/hg/utils/otto/geneReviews/geneReviewsWrapper.sh
  • lines changed 8, context: html, text, full: html, text
    Feature #5522geneReviews track automatic update
    
• src/hg/utils/otto/geneReviews/validateGeneReviews.sh
  • lines changed 36, context: html, text, full: html, text
    Feature #5522geneReviews track automatic update
    
• src/inc/common.mk
  • lines changed 1, context: html, text, full: html, text
    Mac OS X Mavericks gcc -Wall complains that openssl is deprecated(Apple wants everyone to use its Common Crypto lib instead).
    Suppress those warnings by adding -Wno-deprecated-declarations
    to HG_WARN for Mac (Darwin).
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v300 final build refs #13064

• lines changed: 838
• files changed: 75