Commits for hiram

v331_base to v332_preview (2016-04-11 to 2016-04-18) v332

• fixup chrM INSDC name refs #17132
  
  • src/hg/makeDb/doc/mm10.txt - lines changed 20, context: html, text, full: html, text
• photographer Oren Peles wikimedia commons via https://commons.wikimedia.org/wiki/User:MathKnight refs #17167
  
  • src/hg/htdocs/images/Rousettus_aegyptiacus.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• beginning rouAeg1 build refs #17167
  
  • src/hg/makeDb/doc/rouAeg1/initialBuild.txt - lines changed 625, context: html, text, full: html, text
• add script to prepare the config.ra file for a genome assembly refs #17167
  
  • src/hg/utils/automation/prepConfig.pl - lines changed 131, context: html, text, full: html, text
• beginning build for galGal5 refs #17168
  
  • src/hg/makeDb/doc/galGal5/initialBuild.txt - lines changed 565, context: html, text, full: html, text
• reorganize to use single genomic.fna.gz file and correct preparation of db.config.ra data refs #17168
  
  • src/hg/utils/automation/prepConfig.pl - lines changed 19, context: html, text, full: html, text
  • src/hg/utils/automation/ucscCompositeAgp.pl - lines changed 22, context: html, text, full: html, text
  • src/hg/utils/automation/unlocalizedWithChroms.pl - lines changed 41, context: html, text, full: html, text
  • src/hg/utils/automation/unplacedWithChroms.pl - lines changed 25, context: html, text, full: html, text
• initial files for galGal5 refs #17168
  
  • src/hg/makeDb/trackDb/chicken/galGal5/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal5/gap.html - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal5/gold.html - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal5/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• correctly set genomeCladePriority refs #17168
  
  • src/hg/utils/automation/prepConfig.pl - lines changed 13, context: html, text, full: html, text
• adding rouAeg1 to the build refs #17167
  
  • src/hg/makeDb/trackDb/bats/rouAeg1/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bats/rouAeg1/gap.html - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bats/rouAeg1/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bats/rouAeg1/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• adding Entrez nuccore link to gold fragment details page refs #17168
  
  • src/hg/hgc/hgc.c - lines changed 1, context: html, text, full: html, text
• fixup INSDC track construction procedure added gold search rule and running RM and TRF refs #17168
  
  • src/hg/makeDb/doc/galGal5/initialBuild.txt - lines changed 147, context: html, text, full: html, text
• added INSDC track and gold assembly search rule and running RM and TRF refs #17167
  
  • src/hg/makeDb/doc/rouAeg1/initialBuild.txt - lines changed 192, context: html, text, full: html, text
• Added galVar1 - Galeopterus variegatus/Malayan flying lemur refs #17180
  
  • 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
• adding rules for galVar1 refs #17180
  
  • src/hg/makeDb/schema/all.joiner - lines changed 10, context: html, text, full: html, text
• done and in the pushQ refs #17180
  
  • src/hg/makeDb/doc/galVar1/initialBuild.txt - lines changed 128, context: html, text, full: html, text
• liftOver from rn3 ro rn6 refs #16879
  
  • src/hg/makeDb/doc/rn3.txt - lines changed 16, context: html, text, full: html, text
• liftOver from felCat3 to felCat8 refs #16879
  
  • src/hg/makeDb/doc/felCat3.txt - lines changed 16, context: html, text, full: html, text
• added blat server refs #17180
  
  • src/hg/makeDb/doc/galVar1/initialBuild.txt - lines changed 13, context: html, text, full: html, text
• Added galGal5; refs #17168
  
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 19, context: html, text, full: html, text
• running genbank refs #17168
  
  • src/hg/makeDb/doc/galGal5/initialBuild.txt - lines changed 162, context: html, text, full: html, text
• fixup galGal5; refs #17168
  
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 1, context: html, text, full: html, text
• liftOver to galGal5 refs #17168
  
  • src/hg/makeDb/doc/galGal4.txt - lines changed 19, context: html, text, full: html, text
• running genbank blatServer assigned and liftOver to galGal4 refs #17168
  
  • src/hg/makeDb/doc/galGal5/initialBuild.txt - lines changed 10, context: html, text, full: html, text
• fixup coding gene selection refs #13673
  
  • src/hg/utils/automation/doNcbiRefSeq.pl - lines changed 9, context: html, text, full: html, text
• v332 preview1 refs #17072
  
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text