Commits for hiram

v321_base to v322_preview (2015-08-24 to 2015-08-31) v322

• Added ci3 Ciona intestnalis; refs #15796
  
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 18, context: html, text, full: html, text
• after phyloFit from 26-way alignment refs #15209
  
  • src/hg/utils/phyloTrees/ce11.26way.nh - lines changed 26, context: html, text, full: html, text
• after phyloFit from 26-way alignment refs #15209
  
  • src/hg/utils/phyloTrees/ce11.26way.scientificNames.nh - lines changed 26, context: html, text, full: html, text
• after phyloFit from 26-way alignment refs #15209
  
  • src/hg/utils/phyloTrees/ce11.commonNames.nh - lines changed 26, context: html, text, full: html, text
• after phyloFit from 26-way alignment refs #15209
  
  • src/hg/utils/phyloTrees/ce11.26way.commonNames.nh - lines changed 26, context: html, text, full: html, text
• common name tree for hg38 100-way refs #14560
  
  • src/hg/htdocs/images/phylo/hg38_100way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• fixing broken names refs #14560
  
  • src/hg/htdocs/images/phylo/hg38_100way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• update brush tailed rat name refs #14560
  
  • src/hg/htdocs/images/phylo/hg38_100way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• adding overrides for chainNet priorities refs #15209
  
  • src/hg/makeDb/trackDb/worm/ancCey1/trackDb.chainNet.ra - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ancCey1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ascSuu1/trackDb.chainNet.ra - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ascSuu1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/bruMal2/trackDb.chainNet.ra - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/bruMal2/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/burXyl1/trackDb.chainNet.ra - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/burXyl1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeAng2/trackDb.chainNet.ra - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeAng2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeJap4/trackDb.chainNet.ra - lines changed 156, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeJap4/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caePb3/trackDb.chainNet.ra - lines changed 156, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caePb3/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeRem4/trackDb.chainNet.ra - lines changed 156, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeRem4/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeSp111/trackDb.chainNet.ra - lines changed 156, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeSp111/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeSp51/trackDb.chainNet.ra - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeSp51/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/cb4/trackDb.chainNet.ra - lines changed 156, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/cb4/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce11/trackDb.chainNet.ra - lines changed 156, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce11/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/dirImm1/trackDb.chainNet.ra - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/dirImm1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/haeCon2/trackDb.chainNet.ra - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/haeCon2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/hetBac1/trackDb.chainNet.ra - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/hetBac1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/loaLoa1/trackDb.chainNet.ra - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/loaLoa1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/melHap1/trackDb.chainNet.ra - lines changed 159, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/melHap1/trackDb.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/melInc2/trackDb.chainNet.ra - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/melInc2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/necAme1/trackDb.chainNet.ra - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/necAme1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/oncVol1/trackDb.chainNet.ra - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/oncVol1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/panRed1/trackDb.chainNet.ra - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/panRed1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/priExs1/trackDb.chainNet.ra - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/priExs1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/priPac3/trackDb.chainNet.ra - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/priPac3/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/strRat2/trackDb.chainNet.ra - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/strRat2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/triSpi1/trackDb.chainNet.ra - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/triSpi1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/triSui1/trackDb.chainNet.ra - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/triSui1/trackDb.ra - lines changed 2, context: html, text, full: html, text
• for calculating chainNet override priorities refs #15209
  
  • src/hg/utils/phyloTrees/ce11.26way.dissect.txt - lines changed 357, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/worms26way.chainNet.pl - lines changed 196, context: html, text, full: html, text
• adding the nematodes and some name corrections refs #15209
  
  • src/hg/utils/phyloTrees/commonNames.sh - lines changed 34, context: html, text, full: html, text
• adding catAur1 chaPel1 nesNot1 podCri1 refs #14560
  
  • src/hg/utils/phyloTrees/scientificNames.sh - lines changed 4, context: html, text, full: html, text
• adding search rules for these new tables refs #13214
  
  • src/hg/makeDb/trackDb/cow/bosTau8/trackDb.ra - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/hedgehog/eriEur2/trackDb.ra - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn6/trackDb.ra - lines changed 10, context: html, text, full: html, text
• procedure for SGP Gene track refs #13214
  
  • src/hg/makeDb/doc/bosTau8.txt - lines changed 25, context: html, text, full: html, text
• updated with geneid search rules refs #13214
  
  • src/hg/makeDb/trackDb/baboon/papAnu2/trackDb.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bonobo/panPan1/trackDb.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat5/trackDb.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro4/trackDb.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam3/trackDb.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/elephant/loxAfr3/trackDb.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gorilla/gorGor3/trackDb.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/horse/equCab2/trackDb.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/orangutan/ponAbe2/trackDb.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rabbit/oryCun2/trackDb.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.ra - lines changed 6, context: html, text, full: html, text
• eliminate stray release alpha tags causing trouble with tdbQuery release checks refs #15209
  
  • src/hg/makeDb/trackDb/trackDb.chainNet.nematode.ra - lines changed 55, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/trackDb.chainNet.ra - lines changed 40, context: html, text, full: html, text
• Added ci3 - Ciona intestinalis refs #15796
  
  • 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 2, context: html, text, full: html, text
• finish removal of ce11.commonNames.sh
  
  • src/hg/utils/phyloTrees/ce11.commonNames.nh - lines changed 26, context: html, text, full: html, text
• adding .soe.ucsc.edu to victim code summary message email To: field refs #15836
  
  • src/utils/qa/weeklybld/doNewBranch.csh - lines changed 1, context: html, text, full: html, text
• Added ancCey1 - A. ceylanicum refs #15209
  
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
• Added ancCeyNames - A. ceylanicum refs #15209
  
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text
• adding ci3 and fixing all the ensGene tracks refs #15796
  
  • src/hg/makeDb/schema/all.joiner - lines changed 25, context: html, text, full: html, text
• fixup the utils-alpha target so it will make binaries in src/utils/ refs #15836
  
  • src/makefile - lines changed 2, context: html, text, full: html, text
• ready for phastCons phyloP runs refs #15209
  
  • src/hg/makeDb/doc/ce11/multiz26way.txt - lines changed 103, context: html, text, full: html, text
• status to DONE from WORKING refs #15524
  
  • src/hg/makeDb/doc/hg38/stsMap.txt - lines changed 1, context: html, text, full: html, text
• capturing data about correspondence between UCSC database and external resources refs #15209
  
  • src/hg/makeDb/doc/genomeCoverage.txt - lines changed 203, context: html, text, full: html, text
  • src/hg/makeDb/doc/genomeInformationSites.txt - lines changed 129, context: html, text, full: html, text
  • src/hg/makeDb/doc/genomeSourceSites.txt - lines changed 149, context: html, text, full: html, text
• v322 preview1 refs #15836
  
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text