File Changes for wong

v255_preview to v255_preview2 (2011-07-26 to 2011-08-02) v255

• src/hg/encode/encodeDownloadReadme/downloadsReadmeTemplate.txt
  • lines changed 45, context: html, text, full: html, text
    made a script to push README file to the download directories
• src/hg/encode/encodeDownloadReadme/encodeDownloadReadme.pl
  • lines changed 160, context: html, text, full: html, text
    made a script to push README file to the download directories
• src/hg/encode/encodeDownloadReadme/makefile
  • lines changed 47, context: html, text, full: html, text
    made a script to push README file to the download directories
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • lines changed 3, context: html, text, full: html, text
    removed the double slashes that broke things in ie
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • lines changed 1, context: html, text, full: html, text
    added pdf.gz support to mkchangenotes
  • lines changed 1, context: html, text, full: html, text
    added in matrix to files only list
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 18, context: html, text, full: html, text
    removed any readme references from doEncodeValidate.pl
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release2.notes
  • lines changed 281, context: html, text, full: html, text
    updated notes file after loading submission
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlLongRnaSeq.release1.notes
  • lines changed 865, context: html, text, full: html, text
    release 1 notes for cshl long
  • lines changed 658, context: html, text, full: html, text
    errors in notes file, duplicates, and some extra files
  • lines changed 64, context: html, text, full: html, text
    removed transcriptgencv7 and corrected amount of new tables
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 7, context: html, text, full: html, text
    put in primer snippet
  • lines changed 6, context: html, text, full: html, text
    removed term fastq
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethylSeq.ra
  • lines changed 57, context: html, text, full: html, text
    removed parentTable to get methyl seq to comply with CV
• src/hg/makeDb/trackDb/human/hg18/wgEncodeSangerGencode.html
  • lines changed 4, context: html, text, full: html, text
    added a reference that was recently published
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 480, context: html, text, full: html, text
    updated rate unrestricted in boradhistone mdb beta and alpha
  • lines changed 319, context: html, text, full: html, text
    reremoved fileindex after syncing the metaDb for date unrestricted required a restore of an earlier version of histone
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 37, context: html, text, full: html, text
    added replacement submissions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    incorrect treatment value for SK-N-SH_RA
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 4, context: html, text, full: html, text
    removed parentTable from affected tracks
  • lines changed 1, context: html, text, full: html, text
    forgot magic number
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 8, context: html, text, full: html, text
    removed parentTable from affected tracks
  • lines changed 1, context: html, text, full: html, text
    forgot magic number
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra
  • lines changed 191, context: html, text, full: html, text
    added 4630 in
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 3, context: html, text, full: html, text
    forgot magic number
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 7, context: html, text, full: html, text
    corrected dateReSubmitted to dateResubmitted
  • lines changed 5, context: html, text, full: html, text
    removed parentTable from affected tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 158, context: html, text, full: html, text
    renamed control for gm12878 + igg-rab to have treatment TNFa
  • lines changed 75, context: html, text, full: html, text
    added missing control to tfbs
  • lines changed 17, context: html, text, full: html, text
    fixed control metadata issues
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUmassDekker5C.ra
  • lines changed 8, context: html, text, full: html, text
    removed parentTable from affected tracks
  • lines changed 1, context: html, text, full: html, text
    forgot magic number
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUw5C.ra
  • lines changed 107, context: html, text, full: html, text
    added stanzas for primer files
  • lines changed 18, context: html, text, full: html, text
    redid the compressed files for matrix gz > tgz
  • lines changed 1, context: html, text, full: html, text
    forgot to generate magic number
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 2, context: html, text, full: html, text
    removed parentTable from affected tracks
  • lines changed 1, context: html, text, full: html, text
    forgot magic number
  • lines changed 1309, context: html, text, full: html, text
    added new tracks for UWTFBS and Histone
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 2362, context: html, text, full: html, text
    added new tracks for UWTFBS and Histone
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeBroadHistone.ra
  • lines changed 77, context: html, text, full: html, text
    updated rate unrestricted in boradhistone mdb beta and alpha
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    removed PAM from default checked
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.html
  • lines changed 6, context: html, text, full: html, text
    added miltuview instructions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.ra
  • lines changed 119, context: html, text, full: html, text
    added 4630 in
  • lines changed 10, context: html, text, full: html, text
    long labels
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.html
  • lines changed 18, context: html, text, full: html, text
    fixed stuff according to redmine #131(QA requests)
  • lines changed 5, context: html, text, full: html, text
    added periods to references
  • lines changed 2, context: html, text, full: html, text
    html cleanup and added line about pooled data
  • lines changed 2, context: html, text, full: html, text
    more html fixes
  • lines changed 2, context: html, text, full: html, text
    more html fixes 2
  • lines changed 1, context: html, text, full: html, text
    new wondie for link
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.ra
  • lines changed 2, context: html, text, full: html, text
    changed cv line, and added tier 1 to cell lines
  • lines changed 1, context: html, text, full: html, text
    fixed stuff according to redmine #131(QA requests)
  • lines changed 1, context: html, text, full: html, text
    changed view limit to match new signal files
  • lines changed 1, context: html, text, full: html, text
    QA corrections
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 2, context: html, text, full: html, text
    renamed control for gm12878 + igg-rab to have treatment TNFa
  • lines changed 11, context: html, text, full: html, text
    added missing control to tfbs
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.html
  • lines changed 3, context: html, text, full: html, text
    put in a line about how primer data must be downloaded to make sense of the matrix
  • lines changed 6, context: html, text, full: html, text
    added release notes for 5c data
  • lines changed 3, context: html, text, full: html, text
    cleaned up filesortorder and correct some html mistakes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.ra
  • lines changed 1, context: html, text, full: html, text
    added view to filesortorder
  • lines changed 1, context: html, text, full: html, text
    cleaned up filesortorder and correct some html mistakes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
  • lines changed 3, context: html, text, full: html, text
    turned off hepg2 default
  • lines changed 7, context: html, text, full: html, text
    changed wi-28 with ohtam treatment to have it's own tag
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
  • lines changed 1, context: html, text, full: html, text
    added new html line
  • lines changed 18, context: html, text, full: html, text
    filled in missing controls
  • lines changed 424, context: html, text, full: html, text
    added new tracks for UWTFBS and Histone
  • lines changed 1, context: html, text, full: html, text
    removed extra 's'
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
  • lines changed 1, context: html, text, full: html, text
    added new html line
  • lines changed 9, context: html, text, full: html, text
    filled in missing controls
  • lines changed 536, context: html, text, full: html, text
    added new tracks for UWTFBS and Histone