Commits for hiram

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

• changing rn4 rules
  • src/hg/hgGene/hgGeneData/otherOrgs.ra - lines changed 3, context: html, text, full: html, text
• add a geneUrl rule to the Rat section
  • src/hg/hgGene/hgGeneData/otherOrgs.ra - lines changed 1, context: html, text, full: html, text
• no otherIdSql needed, the RGD id is ready to go as is
  • src/hg/hgGene/hgGeneData/otherOrgs.ra - lines changed 1, context: html, text, full: html, text
• initial alignment done for 8-way multiz
  • src/hg/makeDb/doc/fr3.txt - lines changed 151, context: html, text, full: html, text
• gap annotated 8-way
  • src/hg/makeDb/doc/fr3.txt - lines changed 106, context: html, text, full: html, text
• frames annotation done on 8-way
  • src/hg/makeDb/doc/fr3.txt - lines changed 103, context: html, text, full: html, text
• phylo tree distance estimate constructed from all_est
  • src/hg/makeDb/doc/fr3.txt - lines changed 142, context: html, text, full: html, text
• construct liftOver from fr2 to fr3
  • src/hg/makeDb/doc/fr2.txt - lines changed 21, context: html, text, full: html, text
• rework the 4d analysis to use ensGenes lifted from fr2, much better branch lengths
  • src/hg/makeDb/doc/fr3.txt - lines changed 34, context: html, text, full: html, text
• only need the .as file, not the .sql file
  • src/hg/lib/kgXrefPrevious.as - lines changed 12, context: html, text, full: html, text
• only need the .as file, not the .sql file
  • src/hg/lib/kgXrefPrevious.sql - lines changed 22, context: html, text, full: html, text
• phastCons and phyloP done
  • src/hg/makeDb/doc/fr3.txt - lines changed 439, context: html, text, full: html, text
• adding 8-way conservation tracks
  • src/hg/makeDb/trackDb/fugu/fr3/trackDb.ra - lines changed 104, context: html, text, full: html, text
• liftover construction ce10 to ce6
  • src/hg/makeDb/doc/ce10.txt - lines changed 17, context: html, text, full: html, text
• add lifted ensGene track from mm9
  • src/hg/makeDb/doc/mm10.txt - lines changed 77, context: html, text, full: html, text
• liftOver pennant icons for fr2 to fr3 and mm9 to mm10
  • src/hg/htdocs/images/2.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/htdocs/images/9.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• liftOver ensGene track from fr2 to fr3
  • src/hg/makeDb/doc/fr3.txt - lines changed 81, context: html, text, full: html, text
• initial source under edit from xenTro3 9-way
  • src/hg/makeDb/trackDb/fugu/fr3/cons8way.html - lines changed 398, context: html, text, full: html, text
• adding lifted ensGene from mm9
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 4, context: html, text, full: html, text
• trackVersion hgFixed entries for ensGene v65
  • src/hg/makeDb/doc/fr3.txt - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 7, context: html, text, full: html, text
• construct hgPal alignment files and download files for 8-way conservation
  • src/hg/makeDb/doc/fr3.txt - lines changed 145, context: html, text, full: html, text
• adding fr3 rules and gadMor1, latCha1 and oreNil1 chains
  • src/hg/makeDb/schema/all.joiner - lines changed 5, context: html, text, full: html, text
• avoid warning errors when maybeSuffix is not defined
  • src/hg/utils/automation/liftRMAlign.pl - lines changed 4, context: html, text, full: html, text
• joinerCheck done, download files, and in the pushQ
  • src/hg/makeDb/doc/fr3.txt - lines changed 25, context: html, text, full: html, text
• cleaned up the assembly description
  • src/hg/makeDb/trackDb/fugu/fr3/description.html - lines changed 45, context: html, text, full: html, text
• up to date with proper information
  • src/hg/makeDb/trackDb/fugu/fr3/gold.html - lines changed 38, context: html, text, full: html, text
• brought up to date
  • src/hg/makeDb/trackDb/fugu/fr3/gap.html - lines changed 49, context: html, text, full: html, text
• adding URL links for external information on this assembly
  • src/hg/makeDb/doc/fr3.txt - lines changed 2, context: html, text, full: html, text
• override for ensGene lifted indicator and update 8-way description
  • src/hg/makeDb/trackDb/fugu/fr3/cons8way.html - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/fr3/trackDb.ra - lines changed 4, context: html, text, full: html, text