Commits for cricket

v264_preview2 to v264_base (2012-02-28 to 2012-03-06) v264

• Getting rid of the last .new file
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.new.ra - lines changed 343, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.release2.ra - lines changed 343, context: html, text, full: html, text
• Staging all of the other assemblies to have metaDb dirs instead of metaDb in the files
  • src/hg/makeDb/trackDb/chimp/panTro2/metaDb/alpha/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/metaDb/alpha/wgEncodeNhgriBip.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau4/metaDb/alpha/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau4/metaDb/alpha/wgEncodeNhgriBip.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam2/metaDb/alpha/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam2/metaDb/alpha/wgEncodeNhgriBip.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeNhgriBip.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn4/metaDb/alpha/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn4/metaDb/alpha/wgEncodeNhgriBip.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac2/metaDb/alpha/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac2/metaDb/alpha/wgEncodeNhgriBip.ra - lines changed 14, context: html, text, full: html, text
• Adding basic metaDb for GencodeV11
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV11.ra - lines changed 261, context: html, text, full: html, text
• Adding expIds, accessions, and md5sums. Removing the Freeze information at request of lab
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV11.ra - lines changed 69, context: html, text, full: html, text
• Adding the subId
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV11.ra - lines changed 17, context: html, text, full: html, text
• Adding the GencodeV11 to all.joiner
  • src/hg/makeDb/schema/all.joiner - lines changed 80, context: html, text, full: html, text
• Fixing the Data Release Policy for GENCODE
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.html - lines changed 5, context: html, text, full: html, text
• Changing release policy again.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.html - lines changed 1, context: html, text, full: html, text
• Adding the V11 notes file
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeGencodeV11.release1.notes - lines changed 76, context: html, text, full: html, text
• Commenting out a few tags that seem unused
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.ra - lines changed 2, context: html, text, full: html, text
• Cleaning up the daf for UmassWeng
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUmMassWengTfbsValid.daf - lines changed 25, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUmassWengTfbsValid.daf - lines changed 25, context: html, text, full: html, text
• Changing the green for non-coding to be brighter
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.ra - lines changed 1, context: html, text, full: html, text
• Adding the new composite for UmassWendTfbsValid
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUmassWengTfbsValid.daf - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUMassWengTfbsValid.ra - lines changed 76, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassWengTfbsValid.html - lines changed 84, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassWengTfbsValid.ra - lines changed 11, context: html, text, full: html, text
• This file needs to go to for the UmassWengTfbsValid
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile - lines changed 1, context: html, text, full: html, text
• Adding the Tap information
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.ra - lines changed 378, context: html, text, full: html, text
• Changes according to ticket 6775
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.html - lines changed 48, context: html, text, full: html, text
• Fixing the lab, cell, and dataType to match our CV
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeNhgriBip.ra - lines changed 3, context: html, text, full: html, text
• Finally submitting T98G cell line so I uncommented it
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 52, context: html, text, full: html, text
• Fixes for Steve in #6775
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.html - lines changed 6, context: html, text, full: html, text
• A few more refinements on punctuation and wording for ticket 6775
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.html - lines changed 5, context: html, text, full: html, text