Commits for hiram

v265_preview to v265_preview2 (2012-03-13 to 2012-03-20) v265

• masking done
  • src/hg/makeDb/doc/otoGar3.txt - lines changed 170, context: html, text, full: html, text
• the sort usage message was incorrect
  • src/utils/bedGraphToBigWig/bedGraphToBigWig.c - lines changed 1, context: html, text, full: html, text
• initial files from makeGenomeDb.pl
  • src/hg/makeDb/trackDb/squirrel/speTri2/description.html - lines changed 132, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirrel/speTri2/gap.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirrel/speTri2/gold.html - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirrel/speTri2/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding speTri2 to the build
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• initial browser build
  • src/hg/makeDb/doc/speTri2.txt - lines changed 272, context: html, text, full: html, text
• starting masking procedures
  • src/hg/makeDb/doc/speTri2.txt - lines changed 16, context: html, text, full: html, text
• adding chainNetMm10
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 51, context: html, text, full: html, text
• panTro3, otoGar3, micMur1 lastz done
  • src/hg/makeDb/doc/mm10.txt - lines changed 134, context: html, text, full: html, text
• done with speTri2 hetGla1 dipOrd1 lastz
  • src/hg/makeDb/doc/mm10.txt - lines changed 226, context: html, text, full: html, text
• add NCBI URL information
  • src/hg/makeDb/doc/sarHar1.txt - lines changed 6, context: html, text, full: html, text
• adding URL information to NCBI information pages
  • src/hg/makeDb/doc/ailMel1.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/bosTau7.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/canFam3.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/choHof1.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/dasNov2.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/echTel1.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/eriEur1.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/felCat4.txt - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/galGal4.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/loxAfr3.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/macEug2.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/micMur1.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/myoLuc2.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/ochPri2.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/ornAna1.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/oryCun2.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/oviAri1.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/panTro3.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/petMar1.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/proCap1.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/pteVam1.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/sorAra1.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/speTri1.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/speTri2.txt - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/susScr2.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/taeGut1.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/tarSyr1.txt - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/doc/tupBel1.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/turTru1.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/vicPac1.txt - lines changed 4, context: html, text, full: html, text
• running equCab3 cavPor3 vicPac1 lastz
  • src/hg/makeDb/doc/mm10.txt - lines changed 114, context: html, text, full: html, text
• shell script to replace fasta-subseq command
  • src/hg/utils/automation/fastaSubseq - lines changed 49, context: html, text, full: html, text
• do not need the test reference to fasta-subseq
  • src/hg/utils/automation/fastaSubseq - lines changed 3, context: html, text, full: html, text
• lastz running oryCun2 susScr2 tupBel1 turTru1 vicPac1 and cavPor3
  • src/hg/makeDb/doc/mm10.txt - lines changed 230, context: html, text, full: html, text
• starting lastz runs for choHof1 pteVam1 loxAfr3 felCat4 ailMel1 and canFam3
  • src/hg/makeDb/doc/mm10.txt - lines changed 372, context: html, text, full: html, text
• previous rn5 experiment is now obsolete with new rn5 release
  • src/hg/makeDb/doc/rn5.obsolete.txt - lines changed 361, context: html, text, full: html, text
• there are new included trackDb ra files
  • src/hg/utils/automation/makeGenomeDb.pl - lines changed 2, context: html, text, full: html, text
• updated with new rn5 build original files from makeGenomeDb.pl
  • src/hg/makeDb/trackDb/rat/rn5/gap.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn5/gold.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn5/trackDb.ra - lines changed 25, context: html, text, full: html, text
• adding rn5 to the build
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• buildign a new RN5 release
  • src/hg/makeDb/doc/rn5.txt - lines changed 653, context: html, text, full: html, text