Commits for hiram

v261_preview to v261_preview2 (2011-12-13 to 2011-12-20) v261

• adding gorilla to the xrg definition
  • src/hg/makeDb/schema/all.joiner - lines changed 1, context: html, text, full: html, text
• initial source
  • src/hg/utils/genomeQuality/genomeQuality.pl - lines changed 300, context: html, text, full: html, text
• adding v65 definitions
  • src/hg/utils/automation/EnsGeneAutomate.pm - lines changed 182, context: html, text, full: html, text
• eliminate wget warning: timestamping does nothing in combination with -O. See the manual
  • src/hg/utils/automation/doEnsGeneUpdate.pl - lines changed 4, context: html, text, full: html, text
• update to Ensembl peptide fasta header syntax parsing
  • src/hg/utils/automation/doEnsGeneUpdate.pl - lines changed 1, context: html, text, full: html, text
• version 65 update done
  • src/hg/makeDb/doc/makeEnsembl.txt - lines changed 1030, context: html, text, full: html, text
• version 65 update dateReference updated
  • src/hg/makeDb/doc/makeEnsembl.txt - lines changed 13, context: html, text, full: html, text
• indicate which assemblies are updated in v65
  • src/hg/makeDb/doc/makeEnsembl.txt - lines changed 16, context: html, text, full: html, text
• running a 7-way alignment to eliminate the two broken genomes
  • src/hg/makeDb/doc/ce10.txt - lines changed 833, context: html, text, full: html, text
• 7-way diagram for ce10 multiz
  • src/hg/htdocs/images/phylo/ce10_7way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• adding tracks chainNetFr3 chainNetOreNil1 cons7way chainNetCaePb3 chainNetCaeSp111 chainNetCaeRem4 chainNetCb4 chainNetCaeJap4 chainNetCaeAng1
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 103, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce10/trackDb.ra - lines changed 107, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/trackDb.chainNet.ra - lines changed 306, context: html, text, full: html, text
• adding ce10 and related nematodes
  • src/hg/makeDb/schema/all.joiner - lines changed 17, context: html, text, full: html, text
• fixup color problem for chain net caePb3 tracks on ce10
  • src/hg/hgTracks/netTrack.c - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 1, context: html, text, full: html, text
• fixup errors in the type chain specifications
  • src/hg/makeDb/trackDb/worm/trackDb.chainNet.ra - lines changed 3, context: html, text, full: html, text
• entering pushQ
  • src/hg/makeDb/doc/ce10.txt - lines changed 12, context: html, text, full: html, text
• adding entry for ce10 chain net
  • src/hg/makeDb/trackDb/worm/trackDb.chainNet.ra - lines changed 51, context: html, text, full: html, text
• there is a new panTro4 for v65
  • src/hg/utils/automation/EnsGeneAutomate.pm - lines changed 3, context: html, text, full: html, text
• adding frames creation to the 7-way
  • src/hg/makeDb/doc/ce10.txt - lines changed 53, context: html, text, full: html, text