File Changes for vsmalladi

v255_preview2 to v255_base (2011-08-02 to 2011-08-08) v255

• src/hg/encode/DAFs/2.0/caltechMm9ChipSample.ddf
  • lines changed 9, context: html, text, full: html, text
    Updated caltech Tfbs daf to match what metadata and experiment variable the lab wanted to track. Provided sample DDF. Updated the CV to have differentiation time course registered under treatment. Also add new control term to match to differing readLength of experiments.
• src/hg/encode/DAFs/2.0/caltechMm9Tfbs.daf
  • lines changed 12, context: html, text, full: html, text
    Updated caltech Tfbs daf to match what metadata and experiment variable the lab wanted to track. Provided sample DDF. Updated the CV to have differentiation time course registered under treatment. Also add new control term to match to differing readLength of experiments.
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 1, context: html, text, full: html, text
    Fixed the html printed for preamble to use a relative path to link to correct track configuration page, depending on if you are on hgdownload or hgdownload-test.
  • lines changed 22, context: html, text, full: html, text
    Commented out preamble.html, as this will not be used to generate an index.html page any long. Redmine #4759.
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • lines changed 1, context: html, text, full: html, text
    Added support for tar.gz files to be tracked in notes files.
• src/hg/makeDb/doc/encodeDccHg18/wgEncodeHudsonalphaChipSeq.release3.notes
  • lines changed 3, context: html, text, full: html, text
    Added README.txt and added index.html to the deprecated files list. Also used fileSortOrder to track so that README would work well. Redmine #4558, #3953.
• src/hg/makeDb/doc/encodeDccHg18/wgEncodeUwDnaseSeq.release5.notes.txt
  • lines changed 743, context: html, text, full: html, text
    Added release 5 notes files for track. Redmine #236.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 48, context: html, text, full: html, text
    Updated caltech Tfbs daf to match what metadata and experiment variable the lab wanted to track. Provided sample DDF. Updated the CV to have differentiation time course registered under treatment. Also add new control term to match to differing readLength of experiments.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDnaseSeq.ra
  • lines changed 13, context: html, text, full: html, text
    Added expId's for validation images. Redmine #236
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Added fileSort order for new release. This will work with redirct in new README.txt. Redmine #4633, Redmine #236.
  • lines changed 14, context: html, text, full: html, text
    Removed duplication of includes brought about by incorrect merge resolution.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra
  • lines changed 1, context: html, text, full: html, text
    Added README.txt and added index.html to the deprecated files list. Also used fileSortOrder to track so that README would work well. Redmine #4558, #3953.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.new.html
  • lines changed 3, context: html, text, full: html, text
    Added new release notes that include addition of validation images. Redmine #236
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.new.ra
  • lines changed 1, context: html, text, full: html, text
    Added fileSort order for new release. This will work with redirct in new README.txt. Redmine #4633, Redmine #236.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 3, context: html, text, full: html, text
    Added CalTech TFBS track, so that lab can understand the use of dimensions in for the track. Redmine #3733, note 21.
  • lines changed 4, context: html, text, full: html, text
    Merge branch 'master' into CaltechMm9DafTrial
  • lines changed 4, context: html, text, full: html, text
    Merge branch 'CaltechMm9DafTrial'
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.ra
  • lines changed 105, context: html, text, full: html, text
    Added CalTech TFBS track, so that lab can understand the use of dimensions in for the track. Redmine #3733, note 21.