Commits for hiram

v258_base to v259_preview (2011-10-10 to 2011-10-25) v259

• adding v64 definitions
  • src/hg/utils/automation/EnsGeneAutomate.pm - lines changed 179, context: html, text, full: html, text
• initial contents from makeGenomeDb.pl
  • src/hg/makeDb/trackDb/gorilla/gorGor3/description.html - lines changed 129, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gorilla/gorGor3/gap.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gorilla/gorGor3/gold.html - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gorilla/gorGor3/trackDb.ra - lines changed 40, context: html, text, full: html, text
• adding gorGor3 to the build
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• OK to print Ensembl blue bar link when ucscToEnsembl table exists
  • src/hg/hgTracks/hgTracks.c - lines changed 2, context: html, text, full: html, text
• bosTau4 changes to bosTau6 for ensGeneDb list
  • src/hg/makeDb/schema/all.joiner - lines changed 1, context: html, text, full: html, text
• adding gorGor3 and myoLuc2 to the ensembl gene checks
  • src/hg/makeDb/schema/all.joiner - lines changed 3, context: html, text, full: html, text
• nfsNoodge on the bossScript to allow time for the chmod to take effect
  • src/hg/utils/automation/doHgNearBlastp.pl - lines changed 4, context: html, text, full: html, text
• add an nfsNoodge before the runSSH exec in execute to allow the chmod to percolate thru the NFS system
  • src/hg/utils/automation/HgRemoteScript.pm - lines changed 1, context: html, text, full: html, text
• contents updated to better indicate reality
  • src/hg/makeDb/trackDb/gorilla/gorGor3/description.html - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gorilla/gorGor3/gap.html - lines changed 52, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gorilla/gorGor3/gold.html - lines changed 44, context: html, text, full: html, text
• running simpleRepeats
  • src/hg/makeDb/doc/gorGor3.txt - lines changed 346, context: html, text, full: html, text
• adding ensGene
  • src/hg/makeDb/doc/myoLuc2.txt - lines changed 19, context: html, text, full: html, text
• adding ensGene and ucscToEnsembl tables
  • src/hg/makeDb/doc/bosTau6.txt - lines changed 48, context: html, text, full: html, text
• fix comment copy and paste error
  • src/hg/makeDb/doc/fr2.txt - lines changed 7, context: html, text, full: html, text
• add ctgPos2 track and take out the obsolete all_mrna and all_est definitions
  • src/hg/makeDb/trackDb/gorilla/gorGor3/trackDb.ra - lines changed 31, context: html, text, full: html, text
• beginning v64 ensGene update
  • src/hg/makeDb/doc/makeEnsembl.txt - lines changed 106, context: html, text, full: html, text
• done with masking and getting ready for kluster runs
  • src/hg/makeDb/doc/gorGor3.txt - lines changed 53, context: html, text, full: html, text
• adding gorGor2
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 19, context: html, text, full: html, text
• ready to run genbank when rsync to kluster nodes is done
  • src/hg/makeDb/doc/gorGor3.txt - lines changed 68, context: html, text, full: html, text
• brought this somewhat up to date, work has been abandoned
  • src/hg/makeDb/trackDb/worm/caePb3/description.html - lines changed 73, context: html, text, full: html, text
• starting gorGor3 lastz
  • src/hg/makeDb/doc/hg19.txt - lines changed 63, context: html, text, full: html, text
• daily update for gorGor3 replaces daily update for gorGor2
  • 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
• completed lastz run for gorGor3
  • src/hg/makeDb/doc/hg19.txt - lines changed 6, context: html, text, full: html, text
• genbank done, blatServers setup, and lastz human done
  • src/hg/makeDb/doc/gorGor3.txt - lines changed 40, context: html, text, full: html, text
• adding gorGor3
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 50, context: html, text, full: html, text
• correct phylo placing for all chain and nets on xenTro3
  • src/hg/makeDb/trackDb/xenTro/trackDb.chainNet.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenTro3/trackDb.chainNet.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenTro3/trackDb.ra - lines changed 2, context: html, text, full: html, text
• update the overrides to get chain/net tracks into proper order and correct parameters
  • src/hg/makeDb/trackDb/turkey/trackDb.chainNet.ra - lines changed 34, context: html, text, full: html, text
• running lastz for all primates to gorGor3
  • src/hg/makeDb/doc/calJac3.txt - lines changed 66, context: html, text, full: html, text
  • src/hg/makeDb/doc/gorGor3.txt - lines changed 195, context: html, text, full: html, text
  • src/hg/makeDb/doc/panTro3.txt - lines changed 65, context: html, text, full: html, text
  • src/hg/makeDb/doc/ponAbe2.txt - lines changed 65, context: html, text, full: html, text
  • src/hg/makeDb/doc/rheMac2.txt - lines changed 68, context: html, text, full: html, text
• adding Gibbon - Nomascus leucogenys
  • src/hg/utils/phyloTrees/primates.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/vertebrates.txt - lines changed 1, context: html, text, full: html, text
• improperly interpreting empty fields in infoOut.txt
  • src/hg/utils/automation/extractGtf.pl - lines changed 2, context: html, text, full: html, text
• improperly interpreting empty fields in infoOut.txt
  • src/hg/utils/automation/ensemblInfo.pl - lines changed 1, context: html, text, full: html, text