Commits for vsmalladi

origin/v233_branch to v234_preview (2010-06-07 to 2010-06-15) v234

• Modifed Lab to LICR and grant to Ren, consistent with pi.ra. Changed compiste suffix to LicrChipSeq(not enought data to support just Tfbs) and changed long labels to Ren -> LICR
  • src/hg/encode/DAFs/2.0/renMm9Tfbs.daf - lines changed 7, context: html, text, full: html, text
• Updated the standardized lab UCD(Farnham) -> UCD
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 7, context: html, text, full: html, text
• Checking in the file with the correct information. revision 1.4 was empty accidently. Updated Lab for submission 1122 and 1123 to UCD. Updated UCDavis -> UCD
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 599, context: html, text, full: html, text
• Commented out the specific check for a lab inorder to write replicate to subgroups. The code has been checked in the unit test and will now write replicate as a subgroup regardless of lab. Have discussed with Brian about changes.
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 3, context: html, text, full: html, text
• Removed ; (semicolns) accidently reintrodcued in labVersion
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 12, context: html, text, full: html, text
• Made Lab name consistent for all variants of UCD% -> UCD
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 599, context: html, text, full: html, text
• Made Lab name consistent for all variants of UCD% -> UCD and Harvard(Weissman) -> Harvard
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 81, context: html, text, full: html, text
• Initial check in of Uw Histone( ChIP-seq) metadata file.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra - lines changed 1825, context: html, text, full: html, text
• Updated metaData with metaData for bam from sbumission 1246
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 25, context: html, text, full: html, text
• Updated metaDb to include new bam and broad peak files from June 7th freeze
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 6250, context: html, text, full: html, text
• Updated the metadata line to include only subId and dateSubmitted. updated track and subtrack names to include wgEncode and appropriate abreviations. Lastly updated type wig line to update to ENC-> WGENCODE
  • src/hg/encode/encodeValidate/test/expected/chipseq/trackDb.ra - lines changed 8, context: html, text, full: html, text
• Upated tablenames to include wgEncode
  • src/hg/encode/encodeValidate/test/expected/chipseq/load.ra - lines changed 4, context: html, text, full: html, text
• Updated file names
  • src/hg/encode/encodeValidate/test/expected/chipseq/README.txt - lines changed 2, context: html, text, full: html, text
• Added mdb.txt to check the mdb.txt, might still need to update make file to verify everything in the file
  • src/hg/encode/encodeValidate/test/expected/chipseq/mdb.txt - lines changed 4, context: html, text, full: html, text
• Added fileDb.ra as this is generated by the pipeline at the moment
  • src/hg/encode/encodeValidate/test/expected/chipseq/fileDb.ra - lines changed 16, context: html, text, full: html, text
• Added mdb.txt and fileDb.ra files to check between expected and actual. Uncommented line to print the file name
  • src/hg/encode/encodeValidate/test/makefile - lines changed 2, context: html, text, full: html, text
• Changed fastq format as optional, specified bam files as downloadOnly and standardized compsite name
  • src/hg/encode/DAFs/2.0/uncFaireSeq.daf - lines changed 3, context: html, text, full: html, text
• Added fastq format as optional, specified bam files as downloadOnly and standardized compsite name
  • src/hg/encode/DAFs/2.0/dukeDnaseSeq.daf - lines changed 10, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/utAustinChipSeq.daf - lines changed 11, context: html, text, full: html, text