Commits for cricket

v259_preview to v259_preview2 (2011-10-25 to 2011-11-01) v259

• Making the super track correct and adding the base of a track description
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtFasp.html - lines changed 147, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtFasp.ra - lines changed 2, context: html, text, full: html, text
• Cleaning up labels and such
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra - lines changed 196, context: html, text, full: html, text
• Adding new experiments
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra - lines changed 501, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.new.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.new.ra - lines changed 232, context: html, text, full: html, text
• Adding a reference
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.new.html - lines changed 10, context: html, text, full: html, text
• A was trying to change the antibodies to have the target description, see ticket #1017, I ended up having a very difficult merge conflict surrounding the doner IDs. I think Jeff needs to look at this
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 434, context: html, text, full: html, text
• This is related to ticket 5526 adding the publications
  • src/hg/htdocs/ENCODE/pubs.html - lines changed 38, context: html, text, full: html, text
• Relating to ticket 5523
  • src/hg/htdocs/ENCODE/experiment_guidelines.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/ENCODE/platform_characterization.html - lines changed 2, context: html, text, full: html, text
• removed duplicate lines, I am not sure how this worked with this trackless stanza before, but those lines were redundant
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra - lines changed 8, context: html, text, full: html, text
• This is not a package that we have installed
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, context: html, text, full: html, text
• Fixing the no speacial characters in the tags rule
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra - lines changed 8, context: html, text, full: html, text
• There was a duplicate object in here
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeReg.ra - lines changed 4, context: html, text, full: html, text
• Removing duplicate objects
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 59, context: html, text, full: html, text
• Removing geoAccessions from the trackDB display and adding expIds
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra - lines changed 51, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.new.ra - lines changed 135, context: html, text, full: html, text
• Adding md5sums and changing hgFileUi columns
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.new.ra - lines changed 1, context: html, text, full: html, text
• Related to ticket 5577, removing some obsolete objects and changing a table name
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV4.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra - lines changed 43, context: html, text, full: html, text
• Removing treatment=None to be consistent with previous entires
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra - lines changed 34, context: html, text, full: html, text
• I do not think this line should have been commented out
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, context: html, text, full: html, text
• The first 2 sections of this are ordered.
  • src/hg/htdocs/ENCODE/pubs.html - lines changed 88, context: html, text, full: html, text
• Fixing merge conflict
• Fixing the attic errors
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 64, context: html, text, full: html, text
• Large amounts of citations were added and sorted.
  • src/hg/htdocs/ENCODE/pubs.html - lines changed 754, context: html, text, full: html, text
• added timeout to error message
  • python/lib/ucscgenomics/qa.py - lines changed 1, context: html, text, full: html, text
• Changing the error message and made it not fatal
  • src/hg/encode/qaInit/qaInit - lines changed 2, context: html, text, full: html, text
• Fixing the long labels and removing the preamble from the notes file
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release2.notes - lines changed 1418, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra - lines changed 138, context: html, text, full: html, text
• Shortening long labels
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra - lines changed 7, context: html, text, full: html, text
• Removing to incoorect geoNumbers
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra - lines changed 3, context: html, text, full: html, text
• Staging a new release 3 for this composite.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.new.html - lines changed 1, context: html, text, full: html, text
• Wrong subIDs
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 2, context: html, text, full: html, text
• Fixing merge conflict