All File Changes

v298_preview to v298_preview2 (2014-03-24 to 2014-03-31) v298

• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 6, context: html, text, full: html, text
    adding option to create links back to UCSC for encode .pdf files, refs #11957 and #12717
• src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwUserTable/rsyncEdwUserTable.c
  • lines changed 39, context: html, text, full: html, text
    Write out update statiistics information to log and email message.
• src/hg/hgGene/hgGeneData/Human/links.ra
  • lines changed 7, context: html, text, full: html, text
    add linkouts to Lynx website. #12123
• src/hg/hgMirror/hgMirror
  • lines changed 3, context: html, text, full: html, text
    disactivating udr in hgMirror, refs #11957
  • lines changed 7, context: html, text, full: html, text
    fixing bug in hgMirror where cancel had no effect on current job, refs #11957
  • lines changed 3, context: html, text, full: html, text
    another fix for not working cancel command, refs #11957
  • lines changed 4, context: html, text, full: html, text
    removing --partial option from rsync, refs #11957
  • lines changed 5, context: html, text, full: html, text
    handling invalid jobId, refs #11957
• src/hg/hgTables/mainPage.c
  • lines changed 5, context: html, text, full: html, text
    adding config option to suppress sending output to galaxy or great, refs #12717
  • lines changed 1, context: html, text, full: html, text
    forgot include
• src/hg/hgTracks/bamTrack.c
  • lines changed 6, context: html, text, full: html, text
    added bam track support to gbib, refs #11957, refs #12717(fileName2 is a not a great var name... any better idea?)
    
• src/hg/hgTracks/vcfTrack.c
  • lines changed 20, context: html, text, full: html, text
    Limit vcf filtering for a particular track evsEsp6500, which has slighltly non-conforming vcf fields. Really this code should be changed to not be track specific, but to only offer vcf filters that are requested in trackDb.ra. Redmine #9329.
• src/hg/htdocs/ENCODE/analysisTools.html
  • lines changed 48, context: html, text, full: html, text
    Adding ENCODE tools updates per Mike Pazin, refs# 12863
• src/hg/htdocs/ENCODE/encodeTools.html
  • lines changed 33, context: html, text, full: html, text
    Adding new tools for Mike Pazin to ENCODE Tools, small 10 5 edit refs# 12863
• src/hg/htdocs/ENCODE/experiment_guidelines.html
  • lines changed 1, context: html, text, full: html, text
    ENCODE updates per Mike Pazin, refs# 12863
  • lines changed 1, context: html, text, full: html, text
    Updating updated dates for ENCODE updates refs# 12863
• src/hg/htdocs/ENCODE/qualityMetrics.html
  • lines changed 1, context: html, text, full: html, text
    Small 10 -> 5 edit per Mike Pazin refs# 12863
  • lines changed 1, context: html, text, full: html, text
    Updating updated dates for ENCODE updates refs# 12863
• src/hg/htdocs/ENCODE/terms.html
  • lines changed 54, context: html, text, full: html, text
    ENCODE updates per Mike Pazin, refs# 12863
  • lines changed 2, context: html, text, full: html, text
    Bolding sentence in terms.html for ENCODE per Mike Pazin
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 1, context: html, text, full: html, text
    small change in gbib doc, refs #11957
  • lines changed 8, context: html, text, full: html, text
    updating gbib doc, refs #12834, note 18
  • lines changed 8, context: html, text, full: html, text
    adding one more error message, refs #12834
  • lines changed 87, context: html, text, full: html, text
    adding auto update switch and moving troubleshoot section, refs #11957
  • lines changed 6, context: html, text, full: html, text
    adding note about gbib filenames, refs #12717
• src/hg/htdocs/images/Balaenoptera_acutorostrata_scammoni.jpg
  • lines changed 0, context: html, text, full: html, text
    photo for Minke whale courtesy NOAA via wikicommons refs #12977
• src/hg/lib/hubConnect.c
  • lines changed 2, context: html, text, full: html, text
    some bigger buffers for bigger hubs
  • lines changed 2, context: html, text, full: html, text
    increase the size of a buffer in hubConnect which was killing the100-way assembly hub
    
• src/hg/lib/jksql.c
  • lines changed 2, context: html, text, full: html, text
    small change to jksql for better debug messages, refs #11957
• src/hg/lib/vcfUi.c
  • lines changed 3, context: html, text, full: html, text
    Limit vcf filtering for a particular track evsEsp6500, which has slighltly non-conforming vcf fields. Really this code should be changed to not be track specific, but to only offer vcf filters that are requested in trackDb.ra. Redmine #9329.
• src/hg/makeDb/doc/balAcu1.txt
  • lines changed 49, context: html, text, full: html, text
    starting Minke whale build refs #12977
  • lines changed 44, context: html, text, full: html, text
    initial database is built refs #12977
  • lines changed 140, context: html, text, full: html, text
    running RM and WM, simpleRepeat done refs #12977
• src/hg/makeDb/doc/encodeAwgHg19.txt
  • lines changed 34, context: html, text, full: html, text
    Create metadata and downloads for ENCODE Segmentations. refs #12259:
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeAwgSegmentation.release1.notes
  • lines changed 74, context: html, text, full: html, text
    Add notes file. refs #12259
• src/hg/makeDb/doc/hg19.txt
  • lines changed 115, context: html, text, full: html, text
    Updated to the latest release of Exome Variants. Redmine #9329.
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes15.csh
  • lines changed 10, context: html, text, full: html, text
    add linkouts to Lynx website. #12123
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes14.csh
  • lines changed 7, context: html, text, full: html, text
    fix Kegg tables in mm10, add HTML for knownGeneOld6
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    add hg38 to align.dbs
• src/hg/makeDb/trackDb/balAcu/balAcu1/description.html
  • lines changed 63, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #12977
• src/hg/makeDb/trackDb/balAcu/balAcu1/gap.html
  • lines changed 30, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #12977
• src/hg/makeDb/trackDb/balAcu/balAcu1/gold.html
  • lines changed 34, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #12977
• src/hg/makeDb/trackDb/balAcu/balAcu1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #12977
• src/hg/makeDb/trackDb/drosophila/droYak1/description.html
  • lines changed 1, context: html, text, full: html, text
    changing links on assembly description pages
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    add URL links to genbank accession for the ContigDiff tracks
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
  • lines changed 1, context: html, text, full: html, text
    Correcting small teh -> the typo in 100way html
• src/hg/makeDb/trackDb/human/hg19/evsEsp6500.html
  • lines changed 128, context: html, text, full: html, text
    Added a description page for Exome Variants as delieverd from Qian Yi. #9329.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgSegmentation.ra
  • lines changed 18, context: html, text, full: html, text
    Add files for download to metadata. refs #12259
  • lines changed 37, context: html, text, full: html, text
    Add magic number
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 71, context: html, text, full: html, text
    Correct md5sums found to be wrong during import to new ENCODE data warehouse. refs #10455
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Correct md5sums found to be wrong during import to new ENCODE data warehouse. refs #10455
  • lines changed 1, context: html, text, full: html, text
    Correct md5sums found to be wrong during import to new ENCODE data warehouse. refs #10455
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
  • lines changed 5, context: html, text, full: html, text
    Correct md5sums found to be wrong during import to new ENCODE data warehouse. refs #10455
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 119, context: html, text, full: html, text
    Correct md5sums found to be wrong during import to new ENCODE data warehouse. refs #10455
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 124, context: html, text, full: html, text
    Correct md5sums found to be wrong during import to new ENCODE data warehouse. refs #10455
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    Staging AWG Segmentation track on beta refs# 12979
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeAwgSegmentation.ra
  • lines changed 186, context: html, text, full: html, text
    Staging AWG Segmentation track on beta refs# 12979
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGisRnaPet.ra
  • lines changed 71, context: html, text, full: html, text
    Adding hg19 metaData md5sum changes refs# 10455
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibRnaSeq.ra
  • lines changed 5, context: html, text, full: html, text
    Adding hg19 metaData md5sum changes refs# 10455
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromChip.ra
  • lines changed 119, context: html, text, full: html, text
    Adding hg19 metaData md5sum changes refs# 10455
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRikenCage.ra
  • lines changed 124, context: html, text, full: html, text
    Adding hg19 metaData md5sum changes refs# 10455
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGisRnaPet.ra
  • lines changed 71, context: html, text, full: html, text
    Adding hg19 metaData md5sum changes refs# 10455
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibRnaSeq.ra
  • lines changed 5, context: html, text, full: html, text
    Adding hg19 metaData md5sum changes refs# 10455
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeOpenChromChip.ra
  • lines changed 119, context: html, text, full: html, text
    Adding hg19 metaData md5sum changes refs# 10455
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeRikenCage.ra
  • lines changed 124, context: html, text, full: html, text
    Adding hg19 metaData md5sum changes refs# 10455
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    Added a description page for Exome Variants as delieverd from Qian Yi. #9329.
  • lines changed 4, context: html, text, full: html, text
    add URL links to genbank accession for the ContigDiff tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgSegmentation.html
  • lines changed 281, context: html, text, full: html, text
    Add Credits. Changes from Jason Ernst. General clean-up.
  • lines changed 2, context: html, text, full: html, text
    Fix credits link
  • lines changed 5, context: html, text, full: html, text
    Add ref to existing ChromHMM track. Finishes track description changes based on input from J. Ernst. refs #12259
  • lines changed 4, context: html, text, full: html, text
    Tweaks to track labels and credits, based on feedback from Steven Wilder
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgSegmentation.ra
  • lines changed 2, context: html, text, full: html, text
    Tweak track label
  • lines changed 1, context: html, text, full: html, text
    Trim long label
  • lines changed 2, context: html, text, full: html, text
    Tweaks to track labels and credits, based on feedback from Steven Wilder
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    add URL links to genbank accession for the ContigDiff tracks
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    add balAcu1 Minke whale to the build refs #12977
• src/hg/makeDb/trackDb/mouse/mm10/knownGene.html
  • lines changed 68, context: html, text, full: html, text
    Updated references (redmine #12639)
• src/hg/makeDb/trackDb/mouse/mm10/knownGeneOld6.html
  • lines changed 10, context: html, text, full: html, text
    fix Kegg tables in mm10, add HTML for knownGeneOld6
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechTfbs.ra
  • lines changed 35, context: html, text, full: html, text
    Correct md5sums found to be wrong during import to new ENCODE data warehouse. refs #10455
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 6, context: html, text, full: html, text
    Correct md5sums found to be wrong during import to new ENCODE data warehouse. refs #10455
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeCaltechTfbs.ra
  • lines changed 35, context: html, text, full: html, text
    Adding mm9 metaData md5sum changes refs# 10455
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeCshlLongRnaSeq.ra
  • lines changed 6, context: html, text, full: html, text
    Adding mm9 metaData md5sum changes refs# 10455
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeCaltechTfbs.ra
  • lines changed 35, context: html, text, full: html, text
    Adding mm9 metaData md5sum changes refs# 10455
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeCshlLongRnaSeq.ra
  • lines changed 6, context: html, text, full: html, text
    Adding mm9 metaData md5sum changes refs# 10455
• src/hg/makeDb/trackDb/panda/ailMel1/description.html
  • lines changed 2, context: html, text, full: html, text
    changing links on assembly description pages
• src/hg/makeDb/trackDb/seaHare/aplCal1/description.html
  • lines changed 1, context: html, text, full: html, text
    changing links on assembly description pages
• src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/description.html
  • lines changed 2, context: html, text, full: html, text
    changing links on assembly description pages
• src/hg/makeDb/trackDb/turtle/chrPic1/description.html
  • lines changed 3, context: html, text, full: html, text
    changing links on assembly description pages
• src/hg/utils/makeTableList/makeTableList.c
  • lines changed 6, context: html, text, full: html, text
    making sure that username/password actually works
  • lines changed 9, context: html, text, full: html, text
    there is no userDb/sessionDb table on hgdownload so need to provideoption to connect to hgCentral without cartTablesOk(). refs #11957
    
• src/product/ex.hg.conf
  • lines changed 3, context: html, text, full: html, text
    adding doc for config option from last commit, refs #12717
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v298 preview2 refs #12803

• lines changed: 2845
• files changed: 92