Commits for cricket

v240_base to v241_preview (2010-09-14 to 2010-09-21) v241

• Retiring fields that are not being used anymore, they are commented out for now for wrangler retraining purposes
  • src/hg/encode/encodeValidate/config/fields.ra - lines changed 52, context: html, text, full: html, text
• retiring the term dataAgreementSuffix from all DAFs and fields.ra
  • src/hg/encode/DAFs/2.0/stanfordChipSeq.daf - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/stanfordHg19HistInput.daf - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/stanfordHg19Tfbs.daf - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/stanfordHg19TfbsInput.daf - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/stanfordMm9Tfbs.daf - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/stanfordMm9TfbsInput.daf - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/stanfordNucleosome.daf - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/ucDHg19Hist.daf - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/config/fields.ra - lines changed 5, context: html, text, full: html, text
• removing Chipseq
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 37, context: html, text, full: html, text
• Changed the Yale metaDB to remove relaoded, chromstart, errors in dates, etc
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra - lines changed 3507, context: html, text, full: html, text
• bringing the DAFs up to the most recent submissions
  • src/hg/encode/DAFs/2.0/cshlLongRnaSeq.daf - lines changed 11, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/rikenCageSolexa.daf - lines changed 3, context: html, text, full: html, text
• remove the rnaExtract terms that were not used at Carrie Davis request
  • src/hg/encode/encodeValidate/config/cv.ra - lines changed 15, context: html, text, full: html, text
• adding labProtocolId for Transcriptome Labs
  • src/hg/encode/DAFs/2.0/cshlLongRnaSeq.daf - lines changed 15, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/config/fields.ra - lines changed 8, context: html, text, full: html, text
• unretiring order from fields.ra as it causes doEncodeValidate to fail, add comment on line where I think it needs to be fixed
  • src/hg/encode/DAFs/2.0/cshlLongRnaSeq.daf - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/rikenCageSolexa.daf - lines changed 21, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/config/fields.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/automation/Encode.pm - lines changed 1, context: html, text, full: html, text
• consolidated UCD names from UCDavis UC Davis UCD to UCD(Farnham)
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 127, context: html, text, full: html, text
• fixed katrinas requests in redmine ticket 44
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.html - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.ra - lines changed 5, context: html, text, full: html, text
• Unretireing noAutoCreate, it was hard coded in doEncodeValidate
  • src/hg/encode/encodeValidate/config/fields.ra - lines changed 5, context: html, text, full: html, text
• Changed the if statement about noAutoCreate as we are not auto creating any longer
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, context: html, text, full: html, text
• Changing the if statement to check existance of noAutoCreate variable first
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, context: html, text, full: html, text
• standardize the RNA-seq references
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 734, context: html, text, full: html, text
• Redid type dataType: draft 2
  • src/hg/encode/encodeValidate/config/cv.ra - lines changed 63, context: html, text, full: html, text
• changed DGF to DNaseDgf
  • src/hg/encode/encodeValidate/config/cv.ra - lines changed 3, context: html, text, full: html, text
• changing dataType to be consistent
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 346, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 60, context: html, text, full: html, text