Commits for hiram

v267_preview2 to v267_base (2012-05-08 to 2012-05-15) v267

• Added rn5.
  • 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/rn5.txt - lines changed 87, context: html, text, full: html, text
• Added galGal4.
  • 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
• done with genbank run
  • src/hg/makeDb/doc/galGal4.txt - lines changed 88, context: html, text, full: html, text
• adding: otoGar turTru eriEur gadMor latCha melUnd micMur ochPri oreNil proCap pteVam saiBol sorAra speTri tarSyr tupBel vicPac
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 31, context: html, text, full: html, text
• Added felCat5.
  • 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
• done with genbank run
  • src/hg/makeDb/doc/felCat5.txt - lines changed 89, context: html, text, full: html, text
• adding eriEur1 European hedgehog
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
• adding gadMor1 Atlantic cod
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
• adding latCha1 Coelacanth
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
• Added susScr3.
  • 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
• done with genbank run
  • src/hg/makeDb/doc/susScr3.txt - lines changed 94, context: html, text, full: html, text
• adding melUnd1 budgerigar
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
• adding micMur1 mouse lemur
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
• adding ochPri2 pika
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
• adding oreNil2 Nile tilapia
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
• adding proCap1 Rock hyrax
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
• Added chrPic1.
  • 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
• completed genbank run
  • src/hg/makeDb/doc/chrPic1.txt - lines changed 91, context: html, text, full: html, text
• adding pteVam1 megabat
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
• adding saiBol1 squirrel monkey
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
• additional name for Saimiri boliviensis
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 1, context: html, text, full: html, text
• adding sorAra1 common shrew
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
• adding speTri2 13-lined ground squirrel
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
• speTri AKA Ictidomys tridecemlineatus
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 1, context: html, text, full: html, text
• Added dasNov3.
  • 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
• done with genbank run
  • src/hg/makeDb/doc/dasNov3.txt - lines changed 84, context: html, text, full: html, text
• adding tarSyr1 tarsier
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
• adding tupBel1 tree shrew
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
• adding vicPac1 alpaca
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 18, context: html, text, full: html, text
• Added dipOrd1.
  • 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
• done with genbank run
  • src/hg/makeDb/doc/dipOrd1.txt - lines changed 6, context: html, text, full: html, text
• Added hetGla2.
  • 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
• done with genbank run
  • src/hg/makeDb/doc/hetGla2.txt - lines changed 85, context: html, text, full: html, text
• lifting HapMap recombination maps from hg18
  • src/hg/makeDb/doc/hg19.txt - lines changed 41, context: html, text, full: html, text
• add ignore tables for the ones in decodeRmap
  • src/hg/makeDb/schema/all.joiner - lines changed 16, context: html, text, full: html, text
• Added otoGar3.
  • 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
• liftover to mm9
  • src/hg/makeDb/doc/mm10.txt - lines changed 21, context: html, text, full: html, text
• correct reference to trackDb/README file
  • src/product/README.trackDb - lines changed 1, context: html, text, full: html, text
• Added nomLeu2.
  • 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
• done with genbank run
  • src/hg/makeDb/doc/nomLeu2.txt - lines changed 85, context: html, text, full: html, text
• done with genbank run
  • src/hg/makeDb/doc/otoGar3.txt - lines changed 94, context: html, text, full: html, text
• adding rn5 and chain net Mm10 definitions
  • src/hg/makeDb/schema/all.joiner - lines changed 2, context: html, text, full: html, text
• download files constructed, ready for documentation
  • src/hg/makeDb/doc/rn5.txt - lines changed 7, context: html, text, full: html, text
• adding assemblies: canFam3,chrPic1,dasNov3,felCat5,gadMor1,galGal4,hetGla2,latCha1,melUnd1,nomLeu2,oreNil2,otoGar3,panTro4,papHam1,saiBol1,speTri2,susScr3,triMan1,turTru2
  • src/hg/makeDb/schema/all.joiner - lines changed 22, context: html, text, full: html, text
• fixup missing tables in the new databases just added
  • src/hg/makeDb/schema/all.joiner - lines changed 46, context: html, text, full: html, text
• clean up all errors on the new assemblies recently added
  • src/hg/makeDb/schema/all.joiner - lines changed 9, context: html, text, full: html, text
• Added saiBol1.
  • 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
• done with genbank run
  • src/hg/makeDb/doc/saiBol1.txt - lines changed 90, context: html, text, full: html, text
• Added latCha1.
  • 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
• done with genbank run
  • src/hg/makeDb/doc/latCha1.txt - lines changed 90, context: html, text, full: html, text
• name of doLoad step script is actually doLoad
  • src/hg/utils/automation/doWindowMasker.pl - lines changed 1, context: html, text, full: html, text
• default smallClusterHub is encodek, memk is gone
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 2, context: html, text, full: html, text
• new style minimalist content
  • src/hg/makeDb/trackDb/rat/rn5/description.html - lines changed 106, context: html, text, full: html, text
• dog also has this scientific name
  • src/hg/htdocs/images/Canis_lupus_familiaris.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• new style minimalist content
  • src/hg/makeDb/trackDb/dog/canFam3/description.html - lines changed 106, context: html, text, full: html, text