Commits for fang

v265_preview to v265_preview2 (2012-03-13 to 2012-03-20) v265

• change controlId of a experiment from cell/Input/std to the dccAccession of its input(control) sample
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra - lines changed 574, context: html, text, full: html, text
• update controlId to the dccAccession number of the corresponding input(control) of the experiments.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra - lines changed 345, context: html, text, full: html, text
• add new references for new histone modifications submitted
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.html - lines changed 66, context: html, text, full: html, text
• add references for new histone modifications submitted, the description for histone and tfbs are the same as they are related experiments and thus the references
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.html - lines changed 72, context: html, text, full: html, text
• added md5sums
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra - lines changed 142, context: html, text, full: html, text
• add release2 notes file
  • src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrHistone.release2.notes - lines changed 72, context: html, text, full: html, text
• add correct notes
  • src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrHistone.release2.notes - lines changed 1120, context: html, text, full: html, text
• update release note
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.html - lines changed 1, context: html, text, full: html, text
• added md5sums
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra - lines changed 40, context: html, text, full: html, text
• creating notes file
  • src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrTfbs.release2.notes - lines changed 723, context: html, text, full: html, text
• changing WholeBrain to Whole Brain in subGroup2 cellType, test to see whether this changes the label in the matrix box on the top of the track setting page
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.ra - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• change Whole Brain back to WholeBrain in subgroup2 cellType as it generated err when doing make
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.ra - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• fixed long labels according to Karina's suggestions
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.ra - lines changed 125, context: html, text, full: html, text
• fix more long labels
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.ra - lines changed 8, context: html, text, full: html, text
• fix matrix labeling, remove rna extrack and localization in subtrack listing, fix shortLabel according to Katrina's suggestions, I also removed RNAextract in the file download list
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.ra - lines changed 6, context: html, text, full: html, text
• capitalize the first letter in immortal cells
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.ra - lines changed 1, context: html, text, full: html, text
• clean up labels
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.ra - lines changed 6, context: html, text, full: html, text
• add modification based on Katrina's suggestions
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.html - lines changed 55, context: html, text, full: html, text
• add . in the end of release notes
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.html - lines changed 1, context: html, text, full: html, text
• testing viewLimits setting. see Katrina's question 12 in note #55 in tickiet #6476
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.ra - lines changed 1, context: html, text, full: html, text
• change 0.0 to 3.0 in line starts with type bigWig in BAT rep1 stanza, this is a test to address Katrina's point 12, note #55 in in tickiet #6476
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.ra - lines changed 2, context: html, text, full: html, text
• change 3.0 back to the original value of 0.0 in line starts with type bigWig
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.ra - lines changed 1, context: html, text, full: html, text