Commits for hiram

v266_base to v267_preview (2012-04-24 to 2012-05-01) v267

• fix error in using head in a pipe in csh
  • src/hg/utils/automation/doCpgIslands.pl - lines changed 1, context: html, text, full: html, text
• now taken care of in grcIncidentDb.pl
  • src/hg/utils/automation/ncbiIncidentDb.pl - lines changed 303, context: html, text, full: html, text
• present copy of update.sh used by grcIncidentDb.pl
  • src/hg/utils/automation/grcIncidentUpdate.sh - lines changed 111, context: html, text, full: html, text
• current copy of runUpdate.sh used by grcIncidentDb.pl
  • src/hg/utils/automation/grcRunIncidentUpdate.sh - lines changed 45, context: html, text, full: html, text
• now contained in grcRunIncidentUpdate.sh and grcIncidentUpdate.sh
  • src/hg/utils/automation/ncbiIncidentUpdate.sh - lines changed 83, context: html, text, full: html, text
  • src/hg/utils/automation/ncbiRunIncidentUpdate.sh - lines changed 30, context: html, text, full: html, text
• adding cpgIslandExt track
  • src/hg/makeDb/doc/canFam3.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/choHof1.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/chrPic1.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/dasNov3.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/dipOrd1.txt - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/echTel1.txt - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/doc/eriEur1.txt - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/doc/felCat5.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/fr3.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/gadMor1.txt - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/doc/galGal4.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/hetGla2.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/latCha1.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/melUnd1.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/micMur1.txt - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/nomLeu2.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/ochPri2.txt - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/doc/oreNil1.txt - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/oreNil2.txt - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/otoGar3.txt - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/panTro4.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/papHam1.txt - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/doc/proCap1.txt - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/doc/pteVam1.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/rn5.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/saiBol1.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/sorAra1.txt - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/doc/speTri2.txt - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/susScr3.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/tarSyr1.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/triMan1.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/tupBel1.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/turTru2.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/vicPac1.txt - lines changed 15, context: html, text, full: html, text
• updating comments about which is what
  • src/hg/utils/phyloTrees/placentals.txt - lines changed 30, context: html, text, full: html, text
• update mm9 to mm10
  • src/hg/utils/phyloTrees/60way.nh - lines changed 1, context: html, text, full: html, text
• using bash instead of just sh so the include of browserEnvironment.txt will work without a full path
  • src/product/scripts/allDatabaseUpdate.sh - lines changed 1, context: html, text, full: html, text
  • src/product/scripts/fetchFullGbdb.sh - lines changed 1, context: html, text, full: html, text
  • src/product/scripts/fetchFullGoldenPath.sh - lines changed 1, context: html, text, full: html, text
  • src/product/scripts/fetchMinimalGbdb.sh - lines changed 1, context: html, text, full: html, text
  • src/product/scripts/fetchMinimalGoldenPath.sh - lines changed 1, context: html, text, full: html, text
  • src/product/scripts/kentSrcUpdate.sh - lines changed 1, context: html, text, full: html, text
  • src/product/scripts/loadDb.sh - lines changed 1, context: html, text, full: html, text
  • src/product/scripts/loadUpdateGoldenPath.sh - lines changed 1, context: html, text, full: html, text
  • src/product/scripts/tagGoldenPath.sh - lines changed 1, context: html, text, full: html, text
  • src/product/scripts/updateHtml.sh - lines changed 1, context: html, text, full: html, text
• adding melUnd1 lepOcu1 hapBur1 neoBri1 mayZeb1 punNye1 xipMac1 oreNil1
  • src/hg/utils/phyloTrees/vertebrates.txt - lines changed 26, context: html, text, full: html, text
• similar to doCpgIslands.pl and more robust
  • src/hg/utils/automation/doGenscan.pl - lines changed 354, context: html, text, full: html, text
• properly protect each step from repeats or missing previous step
  • src/hg/utils/automation/doGenscan.pl - lines changed 19, context: html, text, full: html, text
• completed genscan track
  • src/hg/makeDb/doc/canFam3.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/choHof1.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/eriEur1.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/gadMor1.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/hetGla2.txt - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/doc/oreNil1.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/papHam1.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/saiBol1.txt - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/doc/speTri2.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/susScr3.txt - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/tarSyr1.txt - lines changed 12, context: html, text, full: html, text
• vicVic1 is actually vicPac1
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• expand list of chroms for vegaGene redmine 7403
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 1, context: html, text, full: html, text
• done with genscan track build
  • src/hg/makeDb/doc/chrPic1.txt - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/dasNov3.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/dipOrd1.txt - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/doc/echTel1.txt - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/doc/galGal4.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/latCha1.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/melUnd1.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/micMur1.txt - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/doc/nomLeu2.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/ochPri2.txt - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/doc/oreNil2.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/otoGar3.txt - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/proCap1.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/pteVam1.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/rheMac3.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/sorAra1.txt - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/triMan1.txt - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/doc/turTru2.txt - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/doc/vicPac1.txt - lines changed 17, context: html, text, full: html, text