Commits for vsmalladi

v235_base to v236_preview (2010-07-06 to 2010-07-13) v236

• Tim noticed that my added category code had a hole in it and stopped some human submissions. To fix I check if category is defined.
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, context: html, text, full: html, text
• Fixed typo in code that printed Human Cell Line column names the same as mouse.
  • src/hg/encode/hgEncodeVocab/hgEncodeVocab.c - lines changed 1, context: html, text, full: html, text
• Sample DDF for UW Mouse Samples
  • src/hg/encode/DAFs/2.0/uwMm9Sample.ddf - lines changed 10, context: html, text, full: html, text
• Updated hgEncodeVocab to build Mouse Cell Line table according to Mouse specifications. Also made updated links for cell protocols to be ENCODE/protocols/cell/(ogranism) as Melissa. Help from Krish.
  • src/hg/encode/hgEncodeVocab/hgEncodeVocab.c - lines changed 65, context: html, text, full: html, text
• Add category =L cell Line for mouse cell MEL
  • src/hg/encode/encodeValidate/config/cv.ra - lines changed 1, context: html, text, full: html, text
• Accidently used number 0 instead of O when registering DMSO_2.0pct
  • src/hg/encode/encodeValidate/config/cv.ra - lines changed 2, context: html, text, full: html, text
• Updated DAFs, added input instead of control
  • src/hg/encode/DAFs/2.0/stanfordMm9Hist.daf - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/stanfordMm9Tfbs.daf - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/stanfordMm9TfbsInput.daf - lines changed 4, context: html, text, full: html, text
• Updated 5 cell lines that were missing tier designations
  • src/hg/encode/encodeValidate/config/cv.ra - lines changed 5, context: html, text, full: html, text
• Fully updated all mouse DAFs
  • src/hg/encode/DAFs/2.0/stanfordMm9Hist.daf - lines changed 3, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/stanfordMm9Tfbs.daf - lines changed 6, context: html, text, full: html, text
• Added new treatment DMSO_2.0pct
  • src/hg/encode/encodeValidate/config/cv.ra - lines changed 5, context: html, text, full: html, text
• Changed sextype to cellLineSex upon Krishs recomendation
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 5, context: html, text, full: html, text
• Updated doEncodeValidate to take Sex from DDF for tissue samples. Currently will be used for mouse tissues
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 36, context: html, text, full: html, text
• Added new seqPlatform variable to cv.ra and fields.ra to check seqencing platform information for GEO submissions
  • src/hg/encode/encodeValidate/config/cv.ra - lines changed 54, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/config/fields.ra - lines changed 5, context: html, text, full: html, text
• Updated hgEncodeVocab to find path for the valdiation documents for the antibodies now mentioned in cv.ra
  • src/hg/encode/encodeValidate/config/cv.ra - lines changed 18, context: html, text, full: html, text
  • src/hg/encode/hgEncodeVocab/hgEncodeVocab.c - lines changed 2, context: html, text, full: html, text
• Commented out the validation lines that include file names for 2 antibodies
  • src/hg/encode/encodeValidate/config/cv.ra - lines changed 2, context: html, text, full: html, text
• Add age variable that will be submitted by UW Mouse
  • src/hg/encode/DAFs/2.0/uwMm9DnaseSeq.daf - lines changed 1, context: html, text, full: html, text
• Added Mouse labs for Hardison and Stam grants
  • src/hg/encode/encodeValidate/config/pi.ra - lines changed 20, context: html, text, full: html, text
• Updated mouse daf variables to include stain and sex where appropriate
  • src/hg/encode/DAFs/2.0/psuMm95c.daf - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/psuMm9DnaseSeq.daf - lines changed 3, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/psuMm9RnaSeq.daf - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/uwMm9DnaseSeq.daf - lines changed 49, context: html, text, full: html, text
• Updated Mouse Dafs to match controlled vocabulary
  • src/hg/encode/DAFs/2.0/licrMm9Histone.daf - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/licrMm9Tfbs.daf - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/psuMm95c.daf - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/psuMm9DnaseSeq.daf - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/psuMm9Histone.daf - lines changed 3, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/psuMm9RnaSeq.daf - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/psuMm9Tfbs.daf - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/stanfordMm9Hist.daf - lines changed 4, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/stanfordMm9Tfbs.daf - lines changed 3, context: html, text, full: html, text