Commits for cline

v253_base to v254_preview (2011-06-28 to 2011-07-05) v254

• Added several new UW cell protocols
  • src/hg/makeDb/trackDb/cv/alpha/CD34+Mobilized_Stam_protocol.pdf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/trackDb/cv/alpha/HBVP_Stam_protocol.pdf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/trackDb/cv/alpha/HBVSMC_Stam_protocol.pdf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/trackDb/cv/alpha/HMVECdAd_Stam_protocol.pdf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/trackDb/cv/alpha/HPAEC_Stam_protocol.pdf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/trackDb/cv/alpha/NHBE_Stam_protocol.pdf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• Added a script for scraping the cell type wiki table, producing CV stanzas and downloading approved cell protocol documents
  • src/hg/encode/antibodyWikiParser.py - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/cellTypeParser.py - lines changed 195, context: html, text, full: html, text
• Added several new UW cell types
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 130, context: html, text, full: html, text
• replacing the 'decription' of the Fastq stanza with a 'description'
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Fixed the spelling of the name of the Tullius lab
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 3, context: html, text, full: html, text
• Renaming HMVEC_dAd to HMVEC-dAd, for consistency with the rest of the HMVEC cell lines.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Added missing import
  • src/hg/encode/antibodyWikiParser.py - lines changed 1, context: html, text, full: html, text
• During Morgan Gidding's recent visit, it was decided that we'd abandon our old plan of getting the first two subtracks on this track released (saving three additional subtracks for Version 2), and we'd instead try to release all five subtracks as part of Version 1. Accordingly, there's no need anymore to maintain separate .ra and .new.ra files. Getting rid of .new.ra
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra - lines changed 32, context: html, text, full: html, text
• Following on the last commit, getting rid of the .new.ra file to avoid confusion with the .ra file
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.new.ra - lines changed 81, context: html, text, full: html, text
• Following up on the decision to NOT have separate releases of Version 1 of uncBsuProt (with two subtracks) and version 2 (with three additional subtracks), but instead to have one release with all five subtracks. Accordingly, we no longer need to stage separate .ra and .new.ra files. Updated the overall .ra file to reflect this
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 3, context: html, text, full: html, text
• Changing the default subtrack visibility so that the Tier 1 subtracks are all on by default
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra - lines changed 3, context: html, text, full: html, text
• Revised the restrictedUntil dates of two submissions that had been submitted earlier and revoked
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra - lines changed 5, context: html, text, full: html, text
• Updating the release notes for Release 1 of UncBsuProt
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeUncBsuProt.release1.notes - lines changed 22, context: html, text, full: html, text
• Housekeeping: accepted several provisional stanzas, removed one obsolete, commented-out stanza
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 20, context: html, text, full: html, text
• Copying to beta post code review, now that everything looks stable
  • src/hg/makeDb/trackDb/cv/beta/cv.ra - lines changed 1283, context: html, text, full: html, text