Commits for hiram

v248_preview to v248_preview2 (2011-02-22 to 2011-03-01) v248

• done with RM and TRF repeats
  • src/hg/makeDb/doc/panTro3.txt - lines changed 64, context: html, text, full: html, text
• ctgPos2 done and all 'other' gaps are marked
  • src/hg/makeDb/doc/panTro3.txt - lines changed 37, context: html, text, full: html, text
• adding ctgPos2 track
  • src/hg/makeDb/trackDb/chimp/panTro3/ctgPos2.html - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro3/trackDb.ra - lines changed 8, context: html, text, full: html, text
• update numbers and types
  • src/hg/makeDb/trackDb/chimp/panTro3/gap.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro3/gold.html - lines changed 4, context: html, text, full: html, text
• adding panTro3
  • src/hg/makeDb/schema/all.joiner - lines changed 1, context: html, text, full: html, text
• adding panTro3
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 19, context: html, text, full: html, text
• running panTro3 lastz
  • src/hg/makeDb/doc/hg19.txt - lines changed 59, context: html, text, full: html, text
• have rn blat liftOver panTro2 to panTro3
  • src/hg/makeDb/doc/panTro2.txt - lines changed 13, context: html, text, full: html, text
• blat server setup, genbank running lastz with calJac3 and rheMac2 running
  • src/hg/makeDb/doc/panTro3.txt - lines changed 261, context: html, text, full: html, text
• continuing lastz run on panTro3
  • src/hg/makeDb/doc/hg19.txt - lines changed 7, context: html, text, full: html, text
• running lastz rn4
  • src/hg/makeDb/doc/panTro3.txt - lines changed 48, context: html, text, full: html, text
• add panTro3.lift file
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 1, context: html, text, full: html, text
• finished with hg19 panTro3 lastz
  • src/hg/makeDb/doc/hg19.txt - lines changed 10, context: html, text, full: html, text
• lastz running for mm9 ponAbe2 rheMac2 calJac3 equCab2 canFam2 monDom5 galGal3
  • src/hg/makeDb/doc/panTro3.txt - lines changed 352, context: html, text, full: html, text
• construct download files for panTro3 and running cpgIsland
  • src/hg/makeDb/doc/calJac3.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/panTro3.txt - lines changed 97, context: html, text, full: html, text
• adding chain net PanTro3 business
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 50, context: html, text, full: html, text
• cpgIsland track done
  • src/hg/makeDb/doc/panTro3.txt - lines changed 23, context: html, text, full: html, text
• resolve merge conflict
  • src/hg/makeDb/doc/hg19.txt - lines changed 64, context: html, text, full: html, text
• adding panTro3 to the daily update cycle
  • src/hg/makeDb/genbank/etc/align.dbs - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 1, context: html, text, full: html, text
• genbank done
  • src/hg/makeDb/doc/panTro3.txt - lines changed 16, context: html, text, full: html, text
• turn off perChromTables for panTro3
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 1, context: html, text, full: html, text
• no perChrom tables needed for genbank
  • src/hg/makeDb/doc/panTro3.txt - lines changed 2, context: html, text, full: html, text
• remove temporary comment
  • src/hg/makeDb/doc/hg19.txt - lines changed 2, context: html, text, full: html, text
• add matrix to chain and net composites
  • src/hg/makeDb/trackDb/zebrafish/danRer7/trackDb.ra - lines changed 4, context: html, text, full: html, text
• add chain net PanTro3
  • src/hg/makeDb/schema/all.joiner - lines changed 1, context: html, text, full: html, text
• per Mark's advice, move html printout from hdb to hui
  • src/hg/inc/hdb.h - lines changed 7, context: html, text, full: html, text
  • src/hg/inc/hui.h - lines changed 8, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 59, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 59, context: html, text, full: html, text
• genbank reloaded
  • src/hg/makeDb/doc/panTro3.txt - lines changed 1, context: html, text, full: html, text