File Changes for cricket

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

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