Commits for wong

v261_preview to v261_preview2 (2011-12-13 to 2011-12-20) v261

• corrected an error in morgan's modification
  • python/lib/ucscgenomics/ra.py - lines changed 5, context: html, text, full: html, text
• modifications for morgan's new ra.py changes
  • python/lib/ucscgenomics/mkChangeNotes.py - lines changed 1, context: html, text, full: html, text
• filled in the rest of the dccAccessions
  • src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeBroadHistone.ra - lines changed 11, context: html, text, full: html, text
• renamed openchromchip with release tag
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.new.ra - lines changed 1112, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.ra - lines changed 1112, context: html, text, full: html, text
• added in html for open chrom release 2
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.html - lines changed 315, context: html, text, full: html, text
• changed over to release conventions for synth
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.new.ra - lines changed 196, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.ra - lines changed 196, context: html, text, full: html, text
• notes for release2 open chrom synth
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromSynth.release2.notes - lines changed 128, context: html, text, full: html, text
• added in html for synth release 2
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html - lines changed 294, context: html, text, full: html, text
• added in treatment=None values
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra - lines changed 9, context: html, text, full: html, text
• removed unnecessary origAessembly lines
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra - lines changed 17, context: html, text, full: html, text
• added dcc accessions to synth
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra - lines changed 21, context: html, text, full: html, text
• error in making the common set of stanzas, not intersection of self and self, that's just plain wrong
  • python/lib/ucscgenomics/ra.py - lines changed 1, context: html, text, full: html, text
• corrected backward changes
  • python/lib/ucscgenomics/ra.py - lines changed 1, context: html, text, full: html, text
• restored missing metaData form public
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 3586, context: html, text, full: html, text
• added revoke tags to all the restored metadata
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 152, context: html, text, full: html, text
• added md5sums
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 134, context: html, text, full: html, text
• removed stanzas from public that have no files left also added in dccaccessions and expids where possible
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 714, context: html, text, full: html, text
• added bais
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 13, context: html, text, full: html, text
• remade the beta.mdb.ra for riken for dccaccession push
  • src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRikenCage.ra - lines changed 5445, context: html, text, full: html, text
• updated notes to reflect the restoring of revoked data
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release2.notes - lines changed 418, context: html, text, full: html, text
• fleshed out replaced message
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 6, context: html, text, full: html, text
• restored missing stanza from public
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 21, context: html, text, full: html, text
• added md5sums
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 4, context: html, text, full: html, text
• rebuilt the beta.mdb.ra for cshl short's metaData update
  • src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlShortRnaSeq.ra - lines changed 40, context: html, text, full: html, text
• changed comparison to public vs alpha instead of beta vs alpha
  • src/hg/encode/qaUpdateMetadata/qaUpdateMetadata - lines changed 2, context: html, text, full: html, text
• moved progfibro to be near the other fibroblasts
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.ra - lines changed 10, context: html, text, full: html, text
• pre-qa changes for synth
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.ra - lines changed 35, context: html, text, full: html, text
• fixed some metadata issues, added expIds and accessions
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra - lines changed 29, context: html, text, full: html, text
• added md5sum
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra - lines changed 2, context: html, text, full: html, text
• moved comments out of lines with var val pairs
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 18, context: html, text, full: html, text
• cleaned up the restored stanzas, there were many errors
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 74, context: html, text, full: html, text
• fixed some metadata issues caused by reloads
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra - lines changed 5, context: html, text, full: html, text
• fixed regex to be more stringent
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• added obtained by to the subgroups becuase we have colliding objects without it
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.ra - lines changed 112, context: html, text, full: html, text
• open chrom synth release 2 fixes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.ra - lines changed 11, context: html, text, full: html, text
• fixed some interferon descriptions, uncovered problems
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 5, context: html, text, full: html, text
• Revert "Removing the clusters again, we are getting new ones" This reverts commit 09d9948a9918c35ecb5ffe6ba9b2cdd4a12853e6.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 1340, context: html, text, full: html, text
• re-removed clusters from fresh file
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 1267, context: html, text, full: html, text
• forgot to escape the plus last time
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• added release 2 notes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.html - lines changed 5, context: html, text, full: html, text
• batch loaded submissions
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra - lines changed 648, context: html, text, full: html, text
• metadata for batch job
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 1837, context: html, text, full: html, text
• rename to new convention
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra - lines changed 4562, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release4.ra - lines changed 4562, context: html, text, full: html, text
• fixed in trackDb
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
• moved html over
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.html - lines changed 131, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release4.html - lines changed 131, context: html, text, full: html, text
• changed html tag, and collapsed cd20 cell lines into one
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release4.ra - lines changed 4, context: html, text, full: html, text
• changed long labels
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release4.ra - lines changed 54, context: html, text, full: html, text