Commits for vsmalladi

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

• 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/caltechMm9ChipSample.ddf - lines changed 9, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/caltechMm9Tfbs.daf - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 48, context: html, text, full: html, text
• Merge branch 'master' into CaltechMm9DafTrial
• Merge branch 'Development-Mouse' into CaltechMm9DafTrial
• Added CalTech TFBS track, so that lab can understand the use of dimensions in for the track. Redmine #3733, note 21.
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.ra - lines changed 105, context: html, text, full: html, text
• Merge branch 'master' into CaltechMm9DafTrial
• Merge branch 'master' into CaltechMm9DafTrial
• Merge branch 'master' into CaltechMm9DafTrial
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 4, context: html, text, full: html, text
• Merge branch 'Development-Mouse' into CaltechMm9DafTrial
• Merge branch 'master' into CaltechMm9DafTrial
• Merge branch 'master' into CaltechMm9DafTrial
• Merge branch 'master' into CaltechMm9DafTrial
• Merge branch 'master' into CaltechMm9DafTrial
• Merge branch 'master' into CaltechMm9DafTrial
• 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.
  • src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 1, context: html, text, full: html, text
• Merge branch 'CaltechMm9DafTrial'
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 4, 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/encodeLoad/doEncodeLoad.pl - lines changed 22, context: html, text, full: html, text
• Merged in fixes to preamble.html. Added relative link back to track configuration page. Also commented out preamble code so that no new tracks get preamble. This will be replaced with README.txt. Redmine #4759. Merge branch 'PreambleFix'
• Added expId's for validation images. Redmine #236
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDnaseSeq.ra - lines changed 13, 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.html - lines changed 3, context: html, text, full: html, text
• Added support for tar.gz files to be tracked in notes files.
  • src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes - 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/human/hg18/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.new.ra - lines changed 1, context: html, text, full: html, text
• Added release 5 notes files for track. Redmine #236.
  • src/hg/makeDb/doc/encodeDccHg18/wgEncodeUwDnaseSeq.release5.notes.txt - lines changed 743, context: html, text, full: html, text
• Resolved merge conflict.
• Removed duplication of includes brought about by incorrect merge resolution.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 14, 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/wgEncodeHudsonalphaChipSeq.release3.notes - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra - lines changed 1, context: html, text, full: html, text