Commits for hiram

v304_base to v305_preview (2014-08-11 to 2014-08-18) v305

• trying visibility settings refs #13713
  • src/hg/makeDb/trackDb/human/cloneEnd.trackDb.ra - lines changed 80, context: html, text, full: html, text
• tables ignored centromeres for hg38 refs #12689
  • src/hg/makeDb/schema/all.joiner - lines changed 1, context: html, text, full: html, text
• adding methods and credits sections refs #12689
  • src/hg/makeDb/trackDb/human/hg38/centromeres.html - lines changed 31, context: html, text, full: html, text
• adding new assemblies bosTau bucRhi chaVoc cypVar esoLuc halLeu manVit notCor tinGut refs #11636
  • src/hg/utils/phyloTrees/db.ncbiTaxId.tab - lines changed 9, context: html, text, full: html, text
• building genomicSuperDups track refs #13580
  • src/hg/makeDb/doc/hg38.txt - lines changed 43, context: html, text, full: html, text
• adding new orgs corCor manPen refs #11636
  • src/hg/utils/phyloTrees/db.ncbiTaxId.tab - lines changed 2, context: html, text, full: html, text
• adding new orgs hg38 bosTau8 manPen1 chaVoc2 bucRhi1 tinGut2 halLeu1 corCor1 manVit2 phaCar1 croPor0 gavGan0 notCor cypVar1 esoLuc1 refs #11636
  • src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab - lines changed 15, context: html, text, full: html, text
• adding bucRhe1 corCor1 cypVar1 esoLuc1 halLeu1 manPen1 notCor1 refs #10272
  • src/hg/utils/phyloTrees/181way.nh - lines changed 181, context: html, text, full: html, text
• adding bucRhe1 corCor1 cypVar1 esoLuc1 halLeu1 manPen1 notCor1 refs #10272
  • src/hg/utils/phyloTrees/commonNames.sh - lines changed 15, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/makefile - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/scientificNames.sh - lines changed 11, context: html, text, full: html, text
• adding bucRhe1 corCor1 cypVar1 esoLuc1 halLeu1 manPen1 notCor1 refs #10272
  • src/hg/utils/phyloTrees/181way.commonNames.nh - lines changed 181, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/181way.scientificNames.nh - lines changed 181, context: html, text, full: html, text
• correcting a few names refs #10272
  • src/hg/utils/phyloTrees/120way.scientificNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/122way.scientificNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/123way.scientificNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/126way.scientificNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/129way.scientificNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/130way.scientificNames.nh - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/131way.scientificNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/166way.commonNames.nh - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/166way.scientificNames.nh - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/171way.commonNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/171way.scientificNames.nh - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/172way.commonNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/172way.scientificNames.nh - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/174way.commonNames.nh - lines changed 1, context: html, text, full: html, text
• fixup notCor name refs #11636
  • src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab - lines changed 1, context: html, text, full: html, text
• operating the rsync to fetch a new assembly refs #252
  • src/hg/utils/automation/fetchOneNcbi.sh - lines changed 34, context: html, text, full: html, text
• allow maximum length for mirror site builds refs #13792
  • src/hg/lib/chromInfo.sql - lines changed 1, context: html, text, full: html, text
• now with -mito argument to add chrM sequence from genbank id refs #272
  • src/hg/utils/automation/unplacedScaffolds.pl - lines changed 78, context: html, text, full: html, text
• add order key for manPen1 refs #11636
  • src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab - lines changed 1, context: html, text, full: html, text
• simple database and dbDb builds for a database refs #252
  • src/hg/utils/automation/quickDbBuild.sh - lines changed 71, context: html, text, full: html, text
  • src/hg/utils/automation/quickDbdbBuild.sh - lines changed 115, context: html, text, full: html, text
• override for genomicSuperDups to get them into the rep group refs #13580
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 3, context: html, text, full: html, text
• adding galVar Malayan flying lemur and phyCat sperm whale - Physeter catodon refs #10272
  • src/hg/utils/phyloTrees/placentals.txt - lines changed 6, context: html, text, full: html, text
• fixup tricky name mangling refs #10272
  • src/hg/utils/phyloTrees/speciesList.sh - lines changed 2, context: html, text, full: html, text
• allow loading of a different named table refs #9741
  • src/hg/utils/automation/doRepeatMasker.pl - lines changed 31, context: html, text, full: html, text
• v305 preview1 refs #13703
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text