Commits for vsmalladi

v252_base to v253_preview (2011-06-07 to 2011-06-14) v253

• Added back correct definitions for attic that I had accidently trounced commit 48c40b956b858138186093eec647d73a8a6563ac.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 6, context: html, text, full: html, text
• Removed freezeDate from cv and meta-data for Gencode Genes. Updated Data Version to map with version of files in hgdownload-test. Added labExpId to map to GENCODE Version number and to facilitate as a experiment variable, such that each file for GENCODE version will get a different dccAccession number. Update fileSortOrder (downloads page) for GENCODE V4 to show potential for new downloads page with dccAccession numbers. Solves Redmine issue #2390.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeSangerGencode.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencode.ra - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.new.ra - lines changed 129, context: html, text, full: html, text
• renamed Raw to Sig for .bigwig files that were missed previously
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra - lines changed 12, context: html, text, full: html, text
• Updated relase 1 notes that excludes attic gbdb files and tables.
  • src/hg/makeDb/doc/encodeDccMm9/wgEncodeUwDnase.release1.notes - lines changed 89, context: html, text, full: html, text
• Miss counted gbdb files should be 38 and not 31.
  • src/hg/makeDb/doc/encodeDccMm9/wgEncodeUwDnase.release1.notes - lines changed 2, context: html, text, full: html, text
• Merge branch 'Development-Mouse'
• Updated encodeDownloadsPage.pl to support .tgz files. Linked to Attic support. Redmine #2462.
  • src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl - lines changed 1, context: html, text, full: html, text
• To have shorter long labels shortented Embryonic -> Embryo. Also to be consistent with age in short labels substituted A8wks -> 8wks.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra - lines changed 29, context: html, text, full: html, text
• Fixed use of first person in track descriptions. Also fixed use of usually to describe pooling effect.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.html - lines changed 6, context: html, text, full: html, text
• Removed submittedDataVersion because these data are not resubmitted versions of these files but a new version of gencode that can be identified in the labExpId field.
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeSangerGencode.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencode.ra - lines changed 7, context: html, text, full: html, text
• Removed dateUnrestricted, submittedDataVersion, freezeDate. Also added labExpId with the correct GENCODE Version number. This matches the meta-data of the track that is live on hg18. Redmine #2390.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV3.ra - lines changed 3, context: html, text, full: html, text
• Removed use of fileSortOrder and fileUi for track, as this will be repalced by GENCODE V7 on the public browswer.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.new.ra - lines changed 129, context: html, text, full: html, text
• Added the wgEncodeGencodeClassesV3 obj meta-data into the metaData fileName, which previously was not.
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeSangerGencode.ra - lines changed 15, context: html, text, full: html, text
• Merged in changes that solve the Redmine issue #2390. Merge branch 'GencodeGenes'
• Added sex to fields.ra.
  • src/hg/encode/encodeValidate/config/fields.ra - lines changed 7, context: html, text, full: html, text
• Added expId's and dccAccession for 4 mouse tracks.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra - lines changed 341, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra - lines changed 121, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra - lines changed 373, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 571, context: html, text, full: html, text
• Added support for dccAccession=UCSC_Accession in fileSortOrder and fileUi.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra - lines changed 1, context: html, text, full: html, text
• Completley removed the meta-data for experiment with submission 4160.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 49, context: html, text, full: html, text