Commits for vsmalladi

v260_preview2 to v260_base (2011-11-22 to 2011-12-06) v260

• Added new wording for how to access metadata under "Display Conventions and Configuration" sectionfor Redmine #4154 and #4155 based on Redmine # 6083
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.html - lines changed 3, context: html, text, full: html, text
• Fixed some labels that missed when moving labels from beta/cv.ra to public/cv.ra 1. FOS -> eGFP-FOS 2. GATA1 (GATA-1) -> GATA-1 3. GATA1 ( sc-265) -> GATA1 (sc-265) "removed extra space" 4. IKZF1 (IKZF1_(IkN)) ->IKZF1 (IkN) 5. PLU1 (PLU1) -> PLU1 6. TR4 (TR4) -> TR4 7. ELAVL1 (SC-5261) -> ELAVL1 (sc-5261) "lower case sc" 8. SLBP (06-1376; 26522; MA156353) -> SLBP "Need to talk to Jeff about multiple antibodies."
  • src/hg/makeDb/trackDb/cv/public/cv.ra - lines changed 7, context: html, text, full: html, text
• forogt 8. SLBP (06-1376; 26522; MA156353) -> SLBP 'Need to talk to Jeff about multiple antibodies.' in last commit.
  • src/hg/makeDb/trackDb/cv/public/cv.ra - lines changed 1, context: html, text, full: html, text
• Added experiments with 2 new cell lines GM12812 and GM12813. Redmine #4577.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwRepliSeq.ra - lines changed 857, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra - lines changed 181, context: html, text, full: html, text
• Fixes affect Redmine #4154 and #4155 1. Fixed spelling of constructed in "Libraries were contsructed using the Illumina ChIP-seq Sample.." 2. Fixed spelling of chromosomes in "...excluding the _random chromomosomes in the assembly..." 3. Removed reference on how to access meta-data since this is now in View information "(click the down arrow in the subtrack list)"
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.html - lines changed 3, context: html, text, full: html, text
• Re-ran changeNotes since gbdb paths were using /usr/local/apache instead of /gbdb.
  • src/hg/makeDb/doc/encodeDccMm9/wgEncodeCaltechHist.release1.notes - lines changed 18, context: html, text, full: html, text
• Added new Meta description in html files. Redmine #6083.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.new.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.new.html - lines changed 112, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.new.ra - lines changed 1, context: html, text, full: html, text
• Updated bam validation and removed fastq validation, to validate the entire file. Redmine #4156.
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeCaltechRnaSeq.daf - lines changed 2, context: html, text, full: html, text
• Fixes affect Redmine #4155 1. Removed Replicate from filtering and sortOrder, since there is only 1 replicate 2. Made intensity lower case in "... all mapped read Intensity of the signal ... " Above change affects CaltechTfbs track Redmine #4144
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.html - lines changed 1, context: html, text, full: html, text
• These changes have been approved and moved from beta/cv.ra to public. Redmine #6100. Note: This doesn't need to be code reviewed.
  • src/hg/makeDb/trackDb/cv/public/cv.ra - lines changed 93, context: html, text, full: html, text
• Fixed redudant information in long label. Redmine #4155.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.ra - lines changed 1, context: html, text, full: html, text
• Added 2x100 paried-end read for Caltech RNA-Seq track. Redmine #4156.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 5, context: html, text, full: html, text
• Added track description. Redmine #4577.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.html - lines changed 128, context: html, text, full: html, text
• Updated default's on track. Redmine #4577.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra - lines changed 5, context: html, text, full: html, text
• First pass at long and short labels for track. Redmine #4577.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra - lines changed 222, context: html, text, full: html, text
• Updated defaults to be tier 1 and 2 cells. Also updated tags, to force sorting of cells in tier order and alphabetical order. Redmine #4577.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra - lines changed 81, context: html, text, full: html, text
• Fixed broken link on alpha, that had incorrect syntax. Redmine #1012.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Removed links to files that didn't exist and update with missing, which is the standard. Redmine #1012.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 3, context: html, text, full: html, text
• Updated md5sum and expVars. Redmine #4577.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwRepliSeq.ra - lines changed 430, context: html, text, full: html, text
• Added fileSortOrder for track. Redmine #4577.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra - lines changed 1, context: html, text, full: html, text
• Fixed spelling error of methdology. Redmine #4577.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.html - lines changed 1, context: html, text, full: html, text
• Added notes file for first release. Redmine #4577.
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwRepliSeq.release1.notes - lines changed 777, context: html, text, full: html, text
• Added dccAccession and experimentIds for track. 15 unique experiments. Redmine #4577.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwRepliSeq.ra - lines changed 705, context: html, text, full: html, text