hiram: changes by commit

review to branch (2010-03-30 to 2010-04-06) v228

• o_db is sufficient at this time for felCatV17e
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra 1.88 - lines changed: 1, context: html, text, full: html, text
• Fix one last place where long strings in custom tracks cause problems
  • src/hg/hgTracks/wigTrack.c 1.102 - lines changed: 6, context: html, text, full: html, text
• add verbose output to table check to find out who, what, why, where, when
  • src/hg/makeDb/schema/joinerCheck/joinerCheck.c 1.41 - lines changed: 5, context: html, text, full: html, text
• adding susScr2 ailMel1 and fixing up chain checks
  • src/hg/makeDb/schema/all.joiner 1.776 - lines changed: 30, context: html, text, full: html, text
• Added susScr2 - Pig
  • src/hg/makeDb/genbank/etc/align.dbs 1.114 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs 1.118 - lines changed: 1, context: html, text, full: html, text
• susScr2 done and in the pushQ
  • src/hg/makeDb/doc/susScr2.txt 1.3 - lines changed: 231, context: html, text, full: html, text
• adding Sheep OviAra to a 49-way tree
  • src/hg/utils/phyloTrees/49way.dissect.txt 1.1 - lines changed: 679, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/49way.nh 1.1 - lines changed: 23, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNet.pl 1.5 - lines changed: 7, context: html, text, full: html, text
• done and in the pushQ except for the multiz track
  • src/hg/makeDb/doc/calJac3.txt 1.5 - lines changed: 557, context: html, text, full: html, text
• never got susScr1 to work finished with susScr2 lastz
  • src/hg/makeDb/doc/bosTau4.txt 1.23 - lines changed: 59, context: html, text, full: html, text
• have blat server and default location
  • src/hg/makeDb/doc/gorGor2.txt 1.4 - lines changed: 18, context: html, text, full: html, text
• done with Panda ailMel1 lastz
  • src/hg/makeDb/doc/rn4.txt 1.40 - lines changed: 11, context: html, text, full: html, text
• now showing scaffold names
  • src/hg/makeDb/trackDb/marmoset/calJac3/ctgPos2.html 1.1 - lines changed: 16, context: html, text, full: html, text
• adding ctgPos2 track
  • src/hg/makeDb/doc/calJac3.txt 1.6 - lines changed: 45, context: html, text, full: html, text
• initial source
  • src/product/scripts/printEnv.pl 1.1 - lines changed: 25, context: html, text, full: html, text
• adding printEnv.pl
  • src/product/scripts/README 1.3 - lines changed: 2, context: html, text, full: html, text
• finalizing these document pages
  • src/hg/makeDb/trackDb/panda/ailMel1/description.html 1.4 - lines changed: 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/panda/ailMel1/gap.html 1.2 - lines changed: 47, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/panda/ailMel1/gold.html 1.2 - lines changed: 8, context: html, text, full: html, text
• need quotes around a string in a SQL insert statement
  • src/hg/utils/automation/doEnsGeneUpdate.pl 1.24 - lines changed: 3, context: html, text, full: html, text
• Ensembl calJac3 is not our calJac3
  • src/hg/utils/automation/EnsGeneAutomate.pm 1.22 - lines changed: 6, context: html, text, full: html, text
• adding bosTau4ChainPileUp track
  • src/hg/makeDb/trackDb/pig/susScr2/bosTau4ChainPileUp.html 1.1 - lines changed: 50, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pig/susScr2/trackDb.ra 1.2 - lines changed: 7, context: html, text, full: html, text
• can not use shell dollar sign strings in our html files
  • src/hg/makeDb/trackDb/pig/susScr2/bosTau4ChainPileUp.html 1.2 - lines changed: 7, context: html, text, full: html, text
• add wiggle and bedGraph formats for comparison
  • src/hg/makeDb/trackDb/pig/susScr2/trackDb.ra 1.3 - lines changed: 31, context: html, text, full: html, text
• escaping the dollar signs in the html and the backslashes
  • src/hg/makeDb/trackDb/pig/susScr2/bosTau4ChainPileUp.html 1.3 - lines changed: 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pig/susScr2/trackDb.ra 1.4 - lines changed: 2, context: html, text, full: html, text
• allow oryCun2 to find equivalent Ensembl scaffold names for blue bar
  • src/hg/hgTracks/hgTracks.c 1.1636 - lines changed: 9, context: html, text, full: html, text
• finalizing gap,gold descriptions
  • src/hg/makeDb/trackDb/rabbit/oryCun2/gap.html 1.2 - lines changed: 43, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rabbit/oryCun2/gold.html 1.2 - lines changed: 10, context: html, text, full: html, text
• ensGene v57 added and in the pushQ
  • src/hg/makeDb/doc/oryCun2.txt 1.7 - lines changed: 30, context: html, text, full: html, text
• From NCBI taxonomy viewer, species name lists
  • src/hg/utils/phyloTrees/placentals.txt 1.1 - lines changed: 57, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/primates.txt 1.1 - lines changed: 25, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/vertebrates.txt 1.1 - lines changed: 30, context: html, text, full: html, text
• first set of v57 done
  • src/hg/makeDb/doc/makeEnsembl.txt 1.15 - lines changed: 443, context: html, text, full: html, text
• ftp directories have underscore not period for separator
  • src/hg/utils/automation/EnsGeneAutomate.pm 1.23 - lines changed: 50, context: html, text, full: html, text