Commits for hiram

v276_preview to v276_preview2 (2012-11-06 to 2012-11-13) v276

• papAnu2 is the same identity as papHam1
  • src/hg/makeDb/trackDb/makefile - lines changed 2, context: html, text, full: html, text
• 7-way tree image for Lamprey
  • src/hg/htdocs/images/phylo/petMar2_7way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• add note about LOCK TABLES for MySQL 5.5, redmine 9553
  • src/product/README.mysql.setup - lines changed 3, context: html, text, full: html, text
  • src/product/ex.MySQLUserPerms.sh - lines changed 4, context: html, text, full: html, text
• credit BCM with Broad
  • src/hg/makeDb/trackDb/kangarooRat/dipOrd1/description.html - lines changed 1, context: html, text, full: html, text
• remove extra . following May.
  • src/hg/makeDb/trackDb/gadMor/gadMor1/description.html - lines changed 1, context: html, text, full: html, text
• add BCM to NCBI assembly information
  • src/hg/makeDb/trackDb/kangarooRat/dipOrd1/description.html - lines changed 1, context: html, text, full: html, text
• separate petMar chain net for petMar1 and petMar2 different releases
  • src/hg/makeDb/trackDb/chainNetPetMar1.ra - lines changed 50, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chainNetPetMar2.ra - lines changed 50, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/chain.petMar1.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/chain.petMar2.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/net.petMar1.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/net.petMar2.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 100, context: html, text, full: html, text
• completed lastz alignment to mm10
  • src/hg/makeDb/doc/mm10Strains1.txt - lines changed 90, context: html, text, full: html, text
• add bedTail to the allowed composite configuration options, same as bed types
  • src/hg/lib/trackDbCustom.c - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
• add note about Nature paper and 11.5X coverage
  • src/hg/makeDb/doc/braFlo2.txt - lines changed 2, context: html, text, full: html, text
• running white rhino lastz
  • src/hg/makeDb/doc/equCab2.txt - lines changed 54, context: html, text, full: html, text
• download files constructed for the 7-way alignment
  • src/hg/makeDb/doc/petMar2.txt - lines changed 203, context: html, text, full: html, text
• add release tag to override block in medaka petMar1
  • src/hg/makeDb/trackDb/medaka/trackDb.chainNet.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 1, context: html, text, full: html, text
• change table name from mm10Strains1LiftOverPsl to altSeqLiftOverPslStrains1 to help hgc display the sequence
  • src/hg/makeDb/doc/mm10Strains1.txt - lines changed 4, context: html, text, full: html, text
• adding the strains composite track to mm10 and the mm10Locations track to mm10Strains1
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10Strains1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• redmine issue 8707 HTML now reads HTTP
  • src/hg/utils/automation/makeGenomeDb.pl - lines changed 1, context: html, text, full: html, text
• COSMIC v61 update done redmine 9386, and liftOver to hg17, redmine 9571
  • src/hg/makeDb/doc/hg19.txt - lines changed 45, context: html, text, full: html, text
• the alternate strains mapping to the reference, redmine 7341
  • src/hg/makeDb/trackDb/mouse/mm10/mm10Strains1Composite.ra - lines changed 93, context: html, text, full: html, text
• better line wrap in the README files, redmine 8887 note 94
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/automation/makeDownloads.pl - lines changed 10, context: html, text, full: html, text