All File Changes

v277_preview to v277_preview2 (2012-12-03 to 2012-12-11) v277

• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 12, context: html, text, full: html, text
    For Track #8360 (snp137): Steve pointed out that leaf track shortLabelsdon't contain enough identifying info for gene tracks that are part of
    multi-level composites like GENCODE. Add in grandparent and parent
    shortLabel when they aren't already part of the lower levels' shortLabel.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    side png goes into its own directory
• src/hg/htdocs/ENCODE/contacts.html
  • lines changed 1, context: html, text, full: html, text
    Adding Steve to alumni list and alphabetizing contacts for ENCODE and correcting spelling of proteogenomics on FAQformat file section.
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 1, context: html, text, full: html, text
    Adding Steve to alumni list and alphabetizing contacts for ENCODE and correcting spelling of proteogenomics on FAQformat file section.
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 3, context: html, text, full: html, text
    Made changes suggested by Brooke in code review (redmine #9723)
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 47, context: html, text, full: html, text
    Added announcement for SNP137 (redmine #8360)
• src/hg/htdocs/indexNews.html
  • lines changed 83, context: html, text, full: html, text
    Added announcement for SNP137 (redmine #8360)
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v276
• src/hg/lib/trackHub.c
  • lines changed 8, context: html, text, full: html, text
    supertracks were being left out of the track name polishing regime. (#9254)
• src/hg/lib/vcfUi.c
  • lines changed 1, context: html, text, full: html, text
    Removing a bit of wasted vertical space in VCF ui controls.
• src/hg/makeDb/doc/proteins/121210.txt
  • lines changed 702, context: html, text, full: html, text
    start new proteome database
• src/hg/makeDb/doc/rn5.txt
  • lines changed 38, context: html, text, full: html, text
    lastz completed for galGal4 bosTau7 canFam3 ailMel1 panTro4 cavPor3
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes14.csh
  • lines changed 1546, context: html, text, full: html, text
    start build of UCSC genes on hg19
  • lines changed 44, context: html, text, full: html, text
    started UCSC genes v14 for hg19 (#9783)
• src/hg/makeDb/doc/uniProt/sp121210.txt
  • lines changed 57, context: html, text, full: html, text
    start a build of uniProt
• src/hg/makeDb/schema/all.joiner
  • lines changed 33, context: html, text, full: html, text
    Updated rules for ucscRetro tables.
• src/hg/makeDb/trackDb/cow/bosTau3/snp127.html
  • lines changed 2, context: html, text, full: html, text
    Updated journal link; inserted 'www' into the URL for 1000 Genomes (redmine #8360)
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 4, context: html, text, full: html, text
    Renaming validation files for H3K9me3_ab8898 , H3K36me3 , H3K9me3 , H3K4me3 , H3K4me1 , H3K4me3_Abcam Antibodies to match internal mouse validations, RM#9159
  • lines changed 4, context: html, text, full: html, text
    Changing commit a34de24747ca5b11750b29134fc3628312c82ee7, Renaming validation files for H3K9me3_ab8898 , H3K36me3 , H3K9me3 , H3K4me3 , H3K4me1 , H3K4me3_Abcam Antibodies to match internal mouse validations, RM#9159, NOW adding manufacturing antibody numbers too to file names to match existing formats and make file name more specific and clear
  • lines changed 1, context: html, text, full: html, text
    Adding missing protocol for H1-hESC from Jeff Long/Cricket to beta and alpha cv.ra
  • lines changed 1, context: html, text, full: html, text
    Adding manuf# sc-10757 to BAF170 antibody validation file.
  • lines changed 2, context: html, text, full: html, text
    Adding lot# to BATf, and adding validation to BCLAF1, and cleaning up manuf# in validation doc name)
  • lines changed 4, context: html, text, full: html, text
    Adding lot nubmers and A/G affinity purified information to antibodies from project cv.ra cleanup
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 95, context: html, text, full: html, text
    Copying alpha/cv.ra to beta/cv.ra, antibody validation doc changing names and the commenting out of terms not used
  • lines changed 1, context: html, text, full: html, text
    Adding missing protocol for H1-hESC from Jeff Long/Cricket to beta and alpha cv.ra
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 9, context: html, text, full: html, text
    added 2 GSMs to Haib RRBS, finishing up track for #9359
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibMethylRrbs.ra
  • lines changed 9, context: html, text, full: html, text
    Staging GEO numbers for Haib MethylRrbs RM#9359
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibMethylRrbs.ra
  • lines changed 9, context: html, text, full: html, text
    Staging GEO numbers for Haib MethylRrbs RM#9359
• src/hg/makeDb/trackDb/human/hg19/snp130.html
  • lines changed 2, context: html, text, full: html, text
    Updated journal link; inserted 'www' into the URL for 1000 Genomes (redmine #8360)
• src/hg/makeDb/trackDb/human/hg19/snp137.shared.html
  • lines changed 3, context: html, text, full: html, text
    Updated journal link; inserted 'www' into the URL for 1000 Genomes (redmine #8360)
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Updated rheMac2 to rheMac3 so rheMac3 would appear in the Primate Chain/Net track
  • lines changed 53, context: html, text, full: html, text
    Added entry for Retroposed Genes 4.0 track.
  • lines changed 1, context: html, text, full: html, text
    Added date and version number for latest Retroposed Genes track.
• src/hg/makeDb/trackDb/human/hg19/ucscRetroAli4.html
  • lines changed 68, context: html, text, full: html, text
    Description page for Retroposed Genes 4 track.
• src/hg/makeDb/trackDb/miRNA.html
  • lines changed 6, context: html, text, full: html, text
    Made changes suggested by Brooke in code review (redmine #9723)
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.euarchontoglireChainNet.ra
  • lines changed 3, context: html, text, full: html, text
    Changed Chinese_Rhesus to just Rhesus to be consistent with mm10 Conservation track.
• src/hg/makeDb/trackDb/mouse/mm8/miRNA.html
  • lines changed 6, context: html, text, full: html, text
    Made changes suggested by Brooke in code review (redmine #9723)
• src/hg/makeDb/trackDb/mouse/mm9/miRNA.html
  • lines changed 6, context: html, text, full: html, text
    Made changes suggested by Brooke in code review (redmine #9723)
• src/hg/makeDb/trackDb/other/repeats2/trackDb.dnase.ra
  • lines changed 708, context: html, text, full: html, text
    adding encode tracks for repeats2, include files
• src/hg/makeDb/trackDb/other/repeats2/trackDb.histone.ra
  • lines changed 924, context: html, text, full: html, text
    adding encode tracks for repeats2, include files
• src/hg/makeDb/trackDb/other/repeats2/trackDb.ra
  • lines changed 45, context: html, text, full: html, text
    adding knownGenes and genecode to trackDb
  • lines changed 56, context: html, text, full: html, text
    lifting more tracks from hg19
  • lines changed 71, context: html, text, full: html, text
    various pwm track additions for repeats2
  • lines changed 86, context: html, text, full: html, text
    adding encode tracks for repeats2
  • lines changed 22, context: html, text, full: html, text
    sols new data tracks for repeats2 browser
• src/hg/makeDb/trackDb/other/repeats2/trackDb.tf.ra
  • lines changed 846, context: html, text, full: html, text
    adding encode tracks for repeats2, include files
• src/hg/makeDb/trackDb/snp126.html
  • lines changed 3, context: html, text, full: html, text
    Updated journal link; inserted 'www' into the URL for 1000 Genomes (redmine #8360)
• src/hg/makeDb/trackDb/snp127.html
  • lines changed 3, context: html, text, full: html, text
    Updated journal link; inserted 'www' into the URL for 1000 Genomes (redmine #8360)
• src/hg/makeDb/trackDb/snp128.html
  • lines changed 3, context: html, text, full: html, text
    Updated journal link; inserted 'www' into the URL for 1000 Genomes (redmine #8360)
• src/hg/makeDb/trackDb/snp129.html
  • lines changed 3, context: html, text, full: html, text
    Updated journal link; inserted 'www' into the URL for 1000 Genomes (redmine #8360)
• src/hg/makeDb/trackDb/snp130.html
  • lines changed 2, context: html, text, full: html, text
    Updated journal link; inserted 'www' into the URL for 1000 Genomes (redmine #8360)
• src/hg/makeDb/trackDb/snp131.html
  • lines changed 3, context: html, text, full: html, text
    Updated journal link; inserted 'www' into the URL for 1000 Genomes (redmine #8360)
• src/hg/makeDb/trackDb/snp132.shared.html
  • lines changed 3, context: html, text, full: html, text
    Updated journal link; inserted 'www' into the URL for 1000 Genomes (redmine #8360)
• src/hg/makeDb/trackDb/snp135.shared.html
  • lines changed 3, context: html, text, full: html, text
    Updated journal link; inserted 'www' into the URL for 1000 Genomes (redmine #8360)
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Changed visibility setting for SNP135 to hide (redmine #8360)
• src/hg/makeDb/trackDb/worm/ce2/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link
• src/lib/cheapcgi.c
  • lines changed 4, context: html, text, full: html, text
    In cgiMakeCheckboxGroupWithVals's table, put checkboxes in their owncolumns so text doesn't wrap underneath them.
    
• src/lib/htmshell.c
  • lines changed 2, context: html, text, full: html, text
    redmine #8742 Set CHARSET=iso-8859-1 for all hgLogin forms like the hgSession.
• src/product/ex.hg.conf
  • lines changed 9, context: html, text, full: html, text
    no need for udcFuse and adding parallelFetch options
• src/utils/qa/checkGenomeMysql
  • lines changed 1, context: html, text, full: html, text
    Changed check for existence of database to run on genome-mysql instead of using hgsql on the current host. This was failing because the hgcentral table exists on genome-mysql but not on mysqlbeta or hgwdev.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 1, context: html, text, full: html, text
    fixing v277 preview REVIEWDAY to 12-03 instead of incorrect date 11-20
  • lines changed 2, context: html, text, full: html, text
    v277 preview2

• lines changed: 5677
• files changed: 62