Commits for cricket

v252_base to v253_preview (2011-06-07 to 2011-06-14) v253

• Final details from the inventory, removed 1 duplicate experiment, changed the metadata for labExpId J84
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 752, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra - lines changed 9, context: html, text, full: html, text
• cleaned out suspect data references and the metaData (pooled, 1,2) that was failing validate, added a link to the supplimental directory
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 735, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra - lines changed 90, context: html, text, full: html, text
• Cleaning up metaData to match validate. Solexa is dropped and TranscriptGencV3c is fixed where required
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra - lines changed 113, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra - lines changed 13, context: html, text, full: html, text
• adding new view ExonGencV3c
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 6, context: html, text, full: html, text
• Added spikeInLib and corrected run validation
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 11, context: html, text, full: html, text
• Corrected the spelling of auxiliary
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, context: html, text, full: html, text
• Trying to get spikeInPool to work
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 4, context: html, text, full: html, text
• bringing in lost metaData
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 22, context: html, text, full: html, text
• Added protocols
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 2797, context: html, text, full: html, text
• Getting the pipeline to accept spikeIns and to accept doc which is Tim's design
  • src/hg/encode/encodeValidate/config/fields.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 2, context: html, text, full: html, text
• Changed release notes according to #2254
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.html - lines changed 21, context: html, text, full: html, text
• added back missing Contig
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra - lines changed 8, context: html, text, full: html, text
• Fixed a broken link
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.html - lines changed 1, context: html, text, full: html, text
• Trying out new tags for DMSO, they are commented out
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 25, context: html, text, full: html, text
• Depricating LHSR
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExon.new.ra - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExonArray.new.html - lines changed 74, context: html, text, full: html, text
• Fixing broken link
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.html - lines changed 1, context: html, text, full: html, text
• Removing the duplicate of ExonGencV3c
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 6, context: html, text, full: html, text
• Added tier 2 labels and filtering, added origAssembly and dccRep where missing, fixed retinoic acid label
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 473, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra - lines changed 297, context: html, text, full: html, text
• Changeing wranglers around
  • src/hg/encode/encodeValidate/config/labs.ra - lines changed 3, context: html, text, full: html, text
• Small description clarification for release notes
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExonArray.new.html - lines changed 1, context: html, text, full: html, text
• Removed link
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExonArray.new.html - lines changed 5, context: html, text, full: html, text
• added release notes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.html - lines changed 14, context: html, text, full: html, text