Commits for hiram

v275_preview2 to v275_base (2012-10-23 to 2012-10-30) v275

• removing ; from ;: situation in an article reference, redmine 8887 note 64
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 1, context: html, text, full: html, text
• lastz mm10 petMar2 done
  • src/hg/makeDb/doc/mm10.txt - lines changed 66, context: html, text, full: html, text
  • src/hg/makeDb/doc/petMar2.txt - lines changed 22, context: html, text, full: html, text
• adding petMar2 braFlo2 and cerSim1
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 156, context: html, text, full: html, text
• overrides for Mm10 chainNet
  • src/hg/makeDb/trackDb/lamprey/trackDb.chainNet.ra - lines changed 6, context: html, text, full: html, text
• not petMar2 on the proteinAccession identifier
  • src/hg/makeDb/schema/all.joiner - lines changed 1, context: html, text, full: html, text
• default position set and in the pushQ
  • src/hg/makeDb/doc/petMar2.txt - lines changed 8, context: html, text, full: html, text
• remove stray paren, redmine 8887 note 66
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 1, context: html, text, full: html, text
• blat servers assigned
  • src/hg/makeDb/doc/cerSim1.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/petMar2.txt - lines changed 3, context: html, text, full: html, text
• fixup md5sum of axtNet when single file in there, redmine 8887 note 70
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 4, context: html, text, full: html, text
• lastz done for monDom5 and oryLat2
  • src/hg/makeDb/doc/petMar2.txt - lines changed 46, context: html, text, full: html, text
• lastz done to petMar2
  • src/hg/makeDb/doc/oryLat2.txt - lines changed 64, context: html, text, full: html, text
• lastz done hg19 and mm10 to cerSim1
  • src/hg/makeDb/doc/cerSim1.txt - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 60, context: html, text, full: html, text
• duplicate lastz entry for mm10
  • src/hg/makeDb/doc/melUnd1.txt - lines changed 22, context: html, text, full: html, text
• lastz for mm10 swap procedure included here
  • src/hg/makeDb/doc/panTro4.txt - lines changed 22, context: html, text, full: html, text
• fixup some comment names in lastz sections
  • src/hg/makeDb/doc/mm10.txt - lines changed 4, context: html, text, full: html, text
• adding braFlo2
  • src/hg/makeDb/schema/all.joiner - lines changed 9, context: html, text, full: html, text
• fixup labels on naked mole rat lastz
  • src/hg/makeDb/doc/hetGla1.txt - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 3, context: html, text, full: html, text
• brought up to 64-way species
  • src/hg/utils/phyloTrees/64way.nh - lines changed 27, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/64wayChainNet.pl - lines changed 136, context: html, text, full: html, text
• brought up to 64-way species
  • src/hg/utils/phyloTrees/chainNet.pl - lines changed 28, context: html, text, full: html, text
• adding sections for Dolphin, Alpaca, Pig, Coelacanth, Atlantic cod
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 306, context: html, text, full: html, text
• addind in Atlantic Cod gadMor1
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 51, context: html, text, full: html, text
• need 64 way dissect tree
  • src/hg/utils/phyloTrees/64way.dissect.txt - lines changed 889, context: html, text, full: html, text
• adding chiLan1 Chinchilla
  • src/hg/utils/phyloTrees/65way.dissect.txt - lines changed 903, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/65way.nh - lines changed 28, context: html, text, full: html, text
• copy from bin/scripts from March 2006
  • src/hg/utils/automation/extractRepeats - lines changed 73, context: html, text, full: html, text
• done with lastz for chicken lamprey
  • src/hg/makeDb/doc/galGal4.txt - lines changed 65, context: html, text, full: html, text
  • src/hg/makeDb/doc/petMar2.txt - lines changed 19, context: html, text, full: html, text