Commits for hiram

v316_base to v317_preview (2015-05-11 to 2015-05-18) v317

• turning on frames and correct name for phyloP track refs #14560
  
  • src/hg/makeDb/trackDb/human/hg38/trackDb.100way.ra - lines changed 3, context: html, text, full: html, text
• beginning of augustus gene prediction procedure refs #13088
  
  • src/hg/utils/automation/doAugustus.pl - lines changed 395, context: html, text, full: html, text
• now running through cleanup refs #13088
  
  • src/hg/utils/automation/doAugustus.pl - lines changed 55, context: html, text, full: html, text
• now running through cleanup refs #13088
  
  • src/hg/utils/automation/doAugustus.pl - lines changed 1, context: html, text, full: html, text
• now running through cleanup refs #13088
  
  • src/hg/utils/automation/doAugustus.pl - lines changed 2, context: html, text, full: html, text
• adding doAugustus.pl doCpgIslands.pl and doGenscan.pl to the delivered script files list refs #13088
  
  • src/hg/utils/automation/makefile - lines changed 3, context: html, text, full: html, text
• correct README comments for syntenic nets and reciprocal best download files refs #15144
  
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 15, context: html, text, full: html, text
  • src/hg/utils/automation/doRecipBest.pl - lines changed 15, context: html, text, full: html, text
• done with downloads and everything in the pushQ 007537 refs #14560
  
  • src/hg/makeDb/doc/hg38/multiz100way.txt - lines changed 108, context: html, text, full: html, text
• turning on augustusGene track refs #13088
  
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 9, context: html, text, full: html, text
• tweaking documentation refs #14970
  
  • src/hg/makeDb/trackDb/human/hg38/cons20way.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.20way.ra - lines changed 5, context: html, text, full: html, text
• fixup chicken mis reference and add production of rna fasta and protein fasta refs #13088
  
  • src/hg/utils/automation/doAugustus.pl - lines changed 15, context: html, text, full: html, text
• update to correct newer assemblies refs #14560
  
  • src/hg/makeDb/trackDb/human/hg38/cons100way.html - lines changed 8, context: html, text, full: html, text
• use the gp file instead of the database table for the getRnaPred conversions does not always work with the db table refs #13088
  
  • src/hg/utils/automation/doAugustus.pl - lines changed 2, context: html, text, full: html, text
• better batch building fasta and sizing kluster run and gzip result before moving around refs #13088
  
  • src/hg/utils/automation/doAugustus.pl - lines changed 31, context: html, text, full: html, text
• fixing process error procedure refs #13088
  
  • src/hg/utils/automation/doAugustus.pl - lines changed 1, context: html, text, full: html, text
• v317 preview1 refs #15355
  
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text