Commits for wong

v258_preview to v258_preview2 (2011-09-27 to 2011-10-04) v258

• long labels for sydh tfbs
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra - lines changed 17, context: html, text, full: html, text
• short labels sydh tfbs
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra - lines changed 28, context: html, text, full: html, text
• added in 4321 and 4320
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 920, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.new.ra - lines changed 122, context: html, text, full: html, text
• changed alpha to .new.ra for sydh tfbs
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
• added time to EtOH 36Hr treatment. We should consider adding this to the cv, as that term is inconsistent with the others.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra - lines changed 1, context: html, text, full: html, text
• loaded 2 new tracks for sydh Histone
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 257, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.new.ra - lines changed 44, context: html, text, full: html, text
• added 2 new treatments
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 12, context: html, text, full: html, text
• added a lot of haib tfbs tracks
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 2003, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.new.ra - lines changed 381, context: html, text, full: html, text
• added a lot of uw tracks
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra - lines changed 1277, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra - lines changed 441, context: html, text, full: html, text
• changed alpha to html character code
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.new.ra - lines changed 1, context: html, text, full: html, text
• revamped long labels
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.new.ra - lines changed 752, context: html, text, full: html, text
• added in new entries for open chrom dnase
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra - lines changed 451, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.new.ra - lines changed 98, context: html, text, full: html, text
• added in missing no treatments
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.new.ra - lines changed 6, context: html, text, full: html, text
• put it back to the .ra for sydh tfbs
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
• merged non-released release1 with the WIP release2 to be the new release 1
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 184, context: html, text, full: html, text
• objects that needed to be pushed got pushed to release2, uncomment this later
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra - lines changed 30, context: html, text, full: html, text
• updated notes file
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release1.notes - lines changed 184, context: html, text, full: html, text
• removed bad experiments after once-over
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 56, context: html, text, full: html, text
• added md5sums
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 3, context: html, text, full: html, text
• added a lot of DGF tracks
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra - lines changed 813, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra - lines changed 281, context: html, text, full: html, text
• loaded new tracks into release 2 sydh TFBS
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 1409, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra - lines changed 278, context: html, text, full: html, text
• last second revoke and replace of an experiment
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 34, context: html, text, full: html, text
• corrected controls and long labels for replacement experiment
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 2, context: html, text, full: html, text
• added bai's to fileName field.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 23, context: html, text, full: html, text
• updated md5sums
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 63, context: html, text, full: html, text
• removed random accession=hg19 fields
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra - lines changed 108, context: html, text, full: html, text
• updated notes files for unc bsu prot
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeUncBsuProt.release1.notes - lines changed 13, context: html, text, full: html, text
• removed erroneous origAsembly hg19 term
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra - lines changed 5, context: html, text, full: html, text
• cleanup SydhTfbs track
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 14, context: html, text, full: html, text
• cleaned up more trackDb
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 1, context: html, text, full: html, text
• updated notes
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release1.notes - lines changed 89, context: html, text, full: html, text
• updated the info on a replaced track
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra - lines changed 3, context: html, text, full: html, text
• renamed K562/SetDb1/UCD to be consistent with the other objects in the experiment
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 54, context: html, text, full: html, text
• updated notes
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release1.notes - lines changed 7, context: html, text, full: html, text
• put back in lines whose deletion broke things, corrected searchable term in dccRep
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 8, context: html, text, full: html, text
• alpha, beta, public on sydh TFBS trackDb
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
• added in new tracks for open chrom chip
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra - lines changed 336, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.new.ra - lines changed 57, context: html, text, full: html, text
• inserted new antibody terms
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.new.ra - lines changed 1, context: html, text, full: html, text
• added new tracks
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.new.ra - lines changed 180, context: html, text, full: html, text
• added new tracks to broad histone metaDb
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 1162, context: html, text, full: html, text
• added in new haib tracks
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 1184, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.new.ra - lines changed 231, context: html, text, full: html, text
• added in new controls
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 671, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.new.ra - lines changed 82, context: html, text, full: html, text
• added new tracks to Haib methyl 450
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra - lines changed 859, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra - lines changed 353, context: html, text, full: html, text
• removed origAssembly from DGF
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra - lines changed 108, context: html, text, full: html, text
• loaded 2 new borad tracks
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 259, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.new.ra - lines changed 41, context: html, text, full: html, text
• corrected incorrect lab name for antibodies registered.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 9, context: html, text, full: html, text
• missed an antibody
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• cleaned up some whitespace stuff
  • src/hg/encode/encodeDownloadReadme/encodeDownloadReadme.pl - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• fixed long labels UwHistone
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra - lines changed 263, context: html, text, full: html, text
• fixed short labels
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra - lines changed 503, context: html, text, full: html, text
• restored lost metadata
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra - lines changed 115, context: html, text, full: html, text
• changed html for uw histone
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.html - lines changed 14, context: html, text, full: html, text
• fixed longlabels in uwtfbs, added in treatments in uw histone tfbs and cleanup
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra - lines changed 425, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra - lines changed 328, context: html, text, full: html, text
• short labels for uw tfbs
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra - lines changed 236, context: html, text, full: html, text
• restored missing metadata
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra - lines changed 70, context: html, text, full: html, text
• added one track to open chrom dnase
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra - lines changed 118, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.new.ra - lines changed 25, context: html, text, full: html, text
• added in missing non treatment
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.new.ra - lines changed 3, context: html, text, full: html, text
• added in goat control entry
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 5, context: html, text, full: html, text
• added new control to sydh tfbs
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 65, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra - lines changed 11, context: html, text, full: html, text