File Changes for hiram

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

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