Commits for hiram

v271_preview to v271_preview2 (2012-07-24 to 2012-07-31) v271

• hetGla2 done and in the pushQ
  • src/hg/makeDb/doc/hetGla1.txt - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/hetGla2.txt - lines changed 19, context: html, text, full: html, text
• setting default visibilities
  • src/hg/makeDb/trackDb/latCha/latCha1/trackDb.ra - lines changed 11, context: html, text, full: html, text
• done and in the pushQ
  • src/hg/makeDb/doc/latCha1.txt - lines changed 19, context: html, text, full: html, text
• done with liftover to hetGla2
  • src/hg/makeDb/doc/hetGla1.txt - lines changed 1, context: html, text, full: html, text
• setting default visibilities
  • src/hg/makeDb/trackDb/birds/melUnd1/trackDb.ra - lines changed 9, context: html, text, full: html, text
• done and in the pushQ Redmine 6759
  • src/hg/makeDb/doc/melUnd1.txt - lines changed 19, context: html, text, full: html, text
• setting default visibilities
  • src/hg/makeDb/trackDb/mouseLemur/micMur1/trackDb.ra - lines changed 25, context: html, text, full: html, text
• done and in the pushQ, redmine 7675
  • src/hg/makeDb/doc/micMur1.txt - lines changed 17, context: html, text, full: html, text
• setting default track visibilities
  • src/hg/makeDb/trackDb/gibbon/nomLeu2/trackDb.ra - lines changed 5, context: html, text, full: html, text
• done and in the pushQ, redmine 7676
  • src/hg/makeDb/doc/nomLeu2.txt - lines changed 17, context: html, text, full: html, text
• setting default track visibilities
  • src/hg/makeDb/trackDb/pika/ochPri2/trackDb.ra - lines changed 9, context: html, text, full: html, text
• done and in the pushQ, redmine 7677
  • src/hg/makeDb/doc/ochPri2.txt - lines changed 17, context: html, text, full: html, text
• done and in the pushQ, redmine 7678
  • src/hg/makeDb/doc/oreNil2.txt - lines changed 17, context: html, text, full: html, text
• setting default visibilities
  • src/hg/makeDb/trackDb/bushbaby/otoGar3/trackDb.ra - lines changed 9, context: html, text, full: html, text
• done and in the pushQ, redmine 6356
  • src/hg/makeDb/doc/panTro4.txt - lines changed 24, context: html, text, full: html, text
• setting default visibilities
  • src/hg/makeDb/trackDb/baboon/papHam1/trackDb.ra - lines changed 15, context: html, text, full: html, text
• done and in the pushQ, redmine 7669
  • src/hg/makeDb/doc/papHam1.txt - lines changed 24, context: html, text, full: html, text
• set default track visibilities
  • src/hg/makeDb/trackDb/rockHyrax/proCap1/trackDb.ra - lines changed 6, context: html, text, full: html, text
• done and in the pushQ, redmine 7680
  • src/hg/makeDb/doc/proCap1.txt - lines changed 24, context: html, text, full: html, text
• setting default visibilities
  • src/hg/makeDb/trackDb/megabat/pteVam1/trackDb.ra - lines changed 15, context: html, text, full: html, text
• done and in the pushQ, redmine 7681
  • src/hg/makeDb/doc/pteVam1.txt - lines changed 24, context: html, text, full: html, text
• constructed liftOver to panTro4
  • src/hg/makeDb/doc/panTro3.txt - lines changed 14, context: html, text, full: html, text
• adding override for PanTro4
  • src/hg/makeDb/trackDb/rhesus/trackDb.chainNet.ra - lines changed 4, context: html, text, full: html, text
• setting default visibilities for tracks
  • src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.ra - lines changed 14, context: html, text, full: html, text
• adding definition for chainNetPanTro4
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 50, context: html, text, full: html, text
• in the pushQ but maybe not ready to go ?
  • src/hg/makeDb/doc/rheMac3.txt - lines changed 27, context: html, text, full: html, text
• liftOver to Rn5 constructed
  • src/hg/makeDb/doc/rn4.txt - lines changed 15, context: html, text, full: html, text
• liftOver constructed to rheMac3
  • src/hg/makeDb/doc/rheMac2.txt - lines changed 24, context: html, text, full: html, text
• setting default track visibilities
  • src/hg/makeDb/trackDb/saiBol/saiBol1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• done and in the pushQ, redmine 6350
  • src/hg/makeDb/doc/saiBol1.txt - lines changed 24, context: html, text, full: html, text
• setting default track visibilities
  • src/hg/makeDb/trackDb/shrew/sorAra1/trackDb.ra - lines changed 11, context: html, text, full: html, text
• done and in the pushQ, redmine 7682
  • src/hg/makeDb/doc/sorAra1.txt - lines changed 24, context: html, text, full: html, text
• fixing date of operation
  • src/hg/makeDb/doc/saiBol1.txt - lines changed 2, context: html, text, full: html, text
• setting default track visibilities
  • src/hg/makeDb/trackDb/squirrel/speTri2/trackDb.ra - lines changed 12, context: html, text, full: html, text
• done and in the pushQ, redmine 7319
  • src/hg/makeDb/doc/speTri2.txt - lines changed 24, context: html, text, full: html, text
• seting default track visibilities
  • src/hg/makeDb/trackDb/pig/susScr3/trackDb.ra - lines changed 9, context: html, text, full: html, text
• done and in the pushQ, redmine 4015
  • src/hg/makeDb/doc/susScr3.txt - lines changed 24, context: html, text, full: html, text
• setting default track visibilities
  • src/hg/makeDb/trackDb/tarsier/tarSyr1/trackDb.ra - lines changed 15, context: html, text, full: html, text
• done and in the pushQ, redmine 7683
  • src/hg/makeDb/doc/tarSyr1.txt - lines changed 24, context: html, text, full: html, text
• setting default track visibilities
  • src/hg/makeDb/trackDb/manatee/triMan1/trackDb.ra - lines changed 6, context: html, text, full: html, text
• done and in the pushQ, redmine 7684
  • src/hg/makeDb/doc/triMan1.txt - lines changed 24, context: html, text, full: html, text
• done and in the pushQ, redmine 7684
  • src/hg/makeDb/doc/tupBel1.txt - lines changed 24, context: html, text, full: html, text
• setting default track visibilities
  • src/hg/makeDb/trackDb/dolphin/turTru2/trackDb.ra - lines changed 9, context: html, text, full: html, text
• done and in the pushQ, redmine 7686
  • src/hg/makeDb/doc/turTru2.txt - lines changed 25, context: html, text, full: html, text
• setting default track visibilities
  • src/hg/makeDb/trackDb/oreNil/oreNil2/trackDb.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/treeShrew/tupBel1/trackDb.ra - lines changed 16, context: html, text, full: html, text
• setting default track visibilities
  • src/hg/makeDb/trackDb/alpaca/vicPac1/trackDb.ra - lines changed 15, context: html, text, full: html, text
• setting default track visibilities
  • src/hg/makeDb/doc/vicPac1.txt - lines changed 24, context: html, text, full: html, text
• from Wikimedia Commons - Charlesjsharp
  • src/hg/htdocs/images/Geospiza_fortis.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• initial contents from makeGenomeDb.pl
  • src/hg/makeDb/trackDb/birds/geoFor1/description.html - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/geoFor1/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/geoFor1/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/geoFor1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding geoFor1 to the build
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• initial browser build
  • src/hg/makeDb/doc/geoFor1.txt - lines changed 113, context: html, text, full: html, text
• running repeat masker, window masker, simple repeats, all gaps are marked
  • src/hg/makeDb/doc/geoFor1.txt - lines changed 152, context: html, text, full: html, text
• adding geoFor1 medium ground finch
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
• adding definition for geoForNames
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text
• done with masking, starting genbank, cpgIslands and genscan
  • src/hg/makeDb/doc/geoFor1.txt - lines changed 235, context: html, text, full: html, text
• from Wikimedia Commons - Guerin Nicolas
  • src/hg/htdocs/images/Chinchilla_lanigera.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• add medium ground finch geoFor1 and Chinchilla lanigera chiLan
  • src/hg/utils/phyloTrees/placentals.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/vertebrates.txt - lines changed 3, context: html, text, full: html, text
• initial contents from makeGenomeDb.pl
  • src/hg/makeDb/trackDb/chinchilla/chiLan1/description.html - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chinchilla/chiLan1/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chinchilla/chiLan1/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chinchilla/chiLan1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding Chinchilla to the build
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• Added geoFor1.
  • 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 minimal set of tracks
  • src/hg/makeDb/doc/geoFor1.txt - lines changed 32, context: html, text, full: html, text
• adding geoFor1 Medium Ground Finch rules
  • src/hg/makeDb/schema/all.joiner - lines changed 2, context: html, text, full: html, text
• adding genbank usage message
  • src/hg/utils/automation/makeDownloads.pl - lines changed 69, context: html, text, full: html, text
• running repeat masker and window masker
  • src/hg/makeDb/doc/chiLan1.txt - lines changed 366, context: html, text, full: html, text
• adding melUnd1 and geoFor1
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 102, context: html, text, full: html, text
• done with lastz to geoFor1
  • src/hg/makeDb/doc/melGal1.txt - lines changed 57, context: html, text, full: html, text
• completed lastz to geoFor1
  • src/hg/makeDb/doc/hg19.txt - lines changed 64, context: html, text, full: html, text
• done with lastz to geoFor1
  • src/hg/makeDb/doc/mm10.txt - lines changed 61, context: html, text, full: html, text
• done with lastz to geoFor1
  • src/hg/makeDb/doc/melUnd1.txt - lines changed 58, context: html, text, full: html, text
• default RHO position set, downloads and pushQ done, lastz swaps for melUnd1 hg19 mm10 and melGal1
  • src/hg/makeDb/doc/geoFor1.txt - lines changed 121, context: html, text, full: html, text
• liftOver to susScr3 done
  • src/hg/makeDb/doc/susScr2.txt - lines changed 14, context: html, text, full: html, text
• default position set at RHO and pushQ entry done
  • src/hg/makeDb/doc/otoGar3.txt - lines changed 24, context: html, text, full: html, text
• working on lastz to geoFor1
  • src/hg/makeDb/doc/taeGut1.txt - lines changed 57, context: html, text, full: html, text
• working on lastz to geoFor1
  • src/hg/makeDb/doc/galGal4.txt - lines changed 57, context: html, text, full: html, text
• adding chiLan1 Chinchilla
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
• adding definition for chiLanNames
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text
• adding geoFor1 to the chain/net list
  • src/hg/makeDb/schema/all.joiner - lines changed 1, context: html, text, full: html, text
• done with masking and cpgIslands and genscan running genbank
  • src/hg/makeDb/doc/chiLan1.txt - lines changed 87, context: html, text, full: html, text