Commits for vsmalladi

v264_preview to v264_preview2 (2012-02-21 to 2012-02-28) v264

• Added release 2 of track. Redmine #5697.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.html - lines changed 185, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.ra - lines changed 179, context: html, text, full: html, text
• Added 10 experiments for track. Redmine #5697.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUchicagoTfbs.ra - lines changed 2361, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.ra - lines changed 467, context: html, text, full: html, text
• Added 2 more experiments. Redmine #4469.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra - lines changed 239, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.ra - lines changed 73, context: html, text, full: html, text
• Renmaed wgEncodeDukeAffyExon.new.ra -> wgEncodeDukeAffyExon.release3.ra and fixed naming of wgEncodesydhHistone.release3.ra -> wgEncodeSydhHistone.release3.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
• Loaded replaced peaks and hotspots for 18 data sets. At the same time reloaded the Signal tables using the correct View name. Redmine #4468. Note #12.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 61, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.new.ra - lines changed 68, context: html, text, full: html, text
• Updated file names to new release naming structure. Redmine #4468.
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - 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 2634, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.html - lines changed 112, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.ra - lines changed 2634, context: html, text, full: html, text
• Added 6 new submissions. Redmine #4468.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 720, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.ra - lines changed 428, context: html, text, full: html, text
• Added replicate 13 and 14 to attic. Redmine #4468.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.ra - lines changed 49, context: html, text, full: html, text
• Fixed incorrect species name referenced in track description. Redmine #5986.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.html - lines changed 1, context: html, text, full: html, text
• Added release 1 notes for track. Redmine #5986.
  • src/hg/makeDb/doc/encodeDccMm9/wgEncodeCshlLongRnaSeq.release1.notes - lines changed 610, context: html, text, full: html, text
• Making links relative. Redmine #5986.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.html - lines changed 2, context: html, text, full: html, text
• Added 4 cell lines for mouse.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 67, context: html, text, full: html, text
• Fix errors in vendorNames.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 21, context: html, text, full: html, text
• Fixed file name since you can't have / in filenames.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Added missing type to antibody registration.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Updated targets to remove vendorId and removed redudant labels for CycT1 and HMGN1 stating the target twice. Redmine #7060.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 5, context: html, text, full: html, text
• Changed var 'geo' for seqPlatform and platform to geoPlatformName to be more descriptive. Redmine #5111.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 14, context: html, text, full: html, text
• Updated release notes. Redmine #4145.
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeBroadHistone.release2.notes - lines changed 8, context: html, text, full: html, text
• Removed submission 4921, as this duplicated files in 4853 but with incorrect meta-data. Also fixes colliding md5sum issue. Redmine #5397.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 153, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.new.ra - lines changed 18, context: html, text, full: html, text
• Added md5sum's. Redmine #5986.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 7, context: html, text, full: html, text
• Added md5sum's for track. Redmine #4469.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra - lines changed 11, context: html, text, full: html, text
• Updated md5sum's for track. Redmine #4468.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 67, context: html, text, full: html, text
• Updated md5sum's. Redmine #5986.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 143, context: html, text, full: html, text
• Added 3 new differentation treatments. Also updated labels to be consistent on the diffProtA treatments.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 19, context: html, text, full: html, text
• Forgot type treatment.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 3, context: html, text, full: html, text
• Renamed new.ra to release naming schema.
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.new.html - lines changed 173, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.new.ra - lines changed 969, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release3.html - lines changed 173, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release3.ra - lines changed 969, context: html, text, full: html, text
• Renamed files from new to release naming schema. Redmine #5696.
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.new.ra - lines changed 668, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.release2.html - lines changed 154, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.release2.ra - lines changed 669, context: html, text, full: html, text
• Fixes for Redmine #4145 1. Updated Cell line sorting to be by tier 2. Removed treatment on sortable columns as treatment is only in release 3 3. Updated ENCODE data freeze from post ENCODE Jan 2011 Freeze -> Mar 2012 Freeze Redmine #6581
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 458, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release2.ra - lines changed 193, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.ra - lines changed 191, context: html, text, full: html, text
• Fixes in track Description for Redmine #4145 1. Updated sentence from "One to 10 nangograms" -> "A quantity of 1-10 ng" 2. Added phrase 'were added' after "except '-C 11' and '-H output_file'" 3. Added 'was' to phrase "....except for '-e' set to extend..." 4. Changed 'Accession' -> 'UCSC Accession' 5. Addded comma before 'e.g' 6. italicized 'e.g' 7. Changed link to Bernsetin lab to be https 8. Moved Contact to end of credits section and removed period 9. Made journal links to pubmed 10. Updated Data Release Policy to Track Standard
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release2.html - lines changed 54, context: html, text, full: html, text
• Changed post ENCODE Jan 2011 Freeze to ENCODE Mar 2012 Freeze. Redmine #6581.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 58, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 453, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUw5C.ra - lines changed 39, context: html, text, full: html, text
• Fixes in Redmine #4145 1. Changed "A quantity of 1-10 ng of DNA were..." -> "A quantity of 1-10 ng of DNA was" 2. Added phrase 'were added' after "except '-C 11' and '-H output_file'" 3. Changed setence to "...except for '-e' which was set to extend..."
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release2.html - lines changed 3, context: html, text, full: html, text
• Fixed typo in previous commit with change of ENCODE freeze data, left off Freeze. Redmine #6581.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 58, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 453, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUw5C.ra - lines changed 39, context: html, text, full: html, text
• Fixes in Redmine 4145. 14. Fixes typo in restricted until states '2001-10-09' instead of '2009-10-09' 15. Left off 'Freeze' when updating freeze date
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 459, context: html, text, full: html, text
• Updated release 2 from new to release naming. Redmine #4486.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra - lines changed 5901, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.html - lines changed 175, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.ra - lines changed 5902, context: html, text, full: html, text
• Added 25 submissions. Redmine #4486.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 3137, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.ra - lines changed 1041, context: html, text, full: html, text
• Fixed typo in dataVersion found by cronjob.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 3, context: html, text, full: html, text
• Updated object name to include age immortalized for cell lines. Error uncovered by Mike Pazin.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 90, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra - lines changed 77, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.ra - lines changed 49, context: html, text, full: html, text
• Fixes found in Redmine #5986 2. Fixed ordering of Subcutaneous Fat Pad after Stomach 4. Fixed colors of Kidney to be the same color
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.ra - lines changed 4, context: html, text, full: html, text
• Added md5sum's to tracks.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra - lines changed 59, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra - lines changed 62, context: html, text, full: html, text
• 2b. Fixed ordering of Subcutenous Fat Pad in the subTrack list. Redmine #5986.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.ra - lines changed 8, context: html, text, full: html, text
• Removed duplicate key and re-made NHLF stanza.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 36, context: html, text, full: html, text
• Fixes for Redmine #5986 5. Changed sentence from "ENCODE Constoria" -> "ENCODE Consortium" 6. Italicized i.e. 7. Updated last sentence in Tissue Samples to state : "Whenever possible biological replicates were obtained from litermates." Litermates is 1 word 8. Updated .9 -> 0.90 9. Redid citations with qaAddTrackReferences
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.html - lines changed 20, context: html, text, full: html, text
• 7b. Added comma after possible and spelled littermates correctly. Redmine #5986.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.html - lines changed 1, context: html, text, full: html, text
• Removed m from 'possible'. Redmine #5986.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.html - lines changed 1, context: html, text, full: html, text
• Added 3 new differentiation treatments.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 15, context: html, text, full: html, text
• Fixing label for Spikeins to be Spike-ins. Redmine #5986.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Remove duplicate comments that should only be at the end of the stanza. Redmine #7078.
  • src/hg/makeDb/trackDb/cv/public/cv.ra - lines changed 125, context: html, text, full: html, text
• Added 2 new cell lines for Ren lab.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 34, context: html, text, full: html, text
• Misspelled category.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text