Commits for cricket

v260_base to v261_preview (2011-12-06 to 2011-12-13) v261

• Adding a new object and the correct md5sums
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV9.ra - lines changed 42, context: html, text, full: html, text
• The encodeMkChangeNotes fails on Gencode
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeGencodeV9.release1.notes - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• Adding some notes about what i am doing
  • src/hg/makeDb/doc/encodeDccHg19/gencodeV9.txt - lines changed 27, context: html, text, full: html, text
• Making a dummy daf for Gencode
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeGencode.daf - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeGencodeV7.daf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• Adding a GencodeV10 structure, cleaning up v9 notes and submission date
  • src/hg/makeDb/doc/encodeDccHg19/gencodeV9.txt - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV10.ra - lines changed 278, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV9.ra - lines changed 17, context: html, text, full: html, text
• Adding some pubs according to ticket 6090
  • src/hg/htdocs/ENCODE/pubs.html - lines changed 32, context: html, text, full: html, text
• Changing int to a string, I am not sure why this isn't in the cv
  • src/hg/encode/encodeValidate/config/fields.ra - lines changed 6, context: html, text, full: html, text
• removing rnaTreatment and run
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 43, context: html, text, full: html, text
• Removing tags with jeff according to code review
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 28, context: html, text, full: html, text
• Changing the html to not say pooled, dropping the extraFields
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.new.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.new.ra - lines changed 6, context: html, text, full: html, text
• Changing the release structure for Haib RNA Seq
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.html - lines changed 123, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.new.html - lines changed 94, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.new.ra - lines changed 1212, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.release2.html - lines changed 94, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.release2.ra - lines changed 1212, context: html, text, full: html, text
• Upgrading the DAF to have the elements in one daf and the required to be all no
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeRikenCage.daf - lines changed 23, context: html, text, full: html, text
• Adding the V2 data for the broken TssHmm files
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release2.notes - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 145, context: html, text, full: html, text
• Adding the accession and md5sums
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 19, context: html, text, full: html, text
• Bringing some of Flo's words back into this html description of shRNA
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.html - lines changed 7, context: html, text, full: html, text
• Adjusting the DAF to have less expVars
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeHaibRnaSeq.daf - lines changed 4, context: html, text, full: html, text
• Changing details as requested in ticket 1710
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.html - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra - lines changed 188, context: html, text, full: html, text