Commits for max

v313_preview2 to v313_base (2015-03-02 to 2015-03-09) v313

• removing pylint from hgMirror makefile as it adds an additional
  dependency for mirrors.
  
  • src/hg/hgMirror/makefile - lines changed 3, context: html, text, full: html, text
• during its last code review, hgBeacon was criticized,
  partially, because it's calling bigBedInfo and bigBedToBed and so requires
  copies of these in the cgi-bin dir. This change makes hgBeacon easier to
  install as it does not need the external tools anymore.
  It also adds a tester that can be pointed at the hgBeacon to see if it
  works, at least the basic functions.
  It also makes it easier to import VCF files, as it can import these
  directly.
  
  • src/hg/hgBeacon/README.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/hgBeacon/help.txt - lines changed 45, context: html, text, full: html, text
  • src/hg/hgBeacon/hgBeacon - lines changed 511, context: html, text, full: html, text
  • src/hg/hgBeacon/testBeacon - lines changed 68, context: html, text, full: html, text
  • src/utils/bigBedInfo/makefile - lines changed 28, context: html, text, full: html, text
  • src/utils/bigBedToBed/makefile - lines changed 29, context: html, text, full: html, text
• removing utils/ for hgBeacon from the main and the utils makefile
  
  • src/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/makefile - lines changed 14, context: html, text, full: html, text
• removing unnecessary line from the alpha target
  
  • src/makefile - lines changed 1, context: html, text, full: html, text
• making clinvar ottoupdates easier to use
  
  • src/hg/utils/otto/clinvar/clinVarToBed - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/otto/clinvar/doUpdate.sh - lines changed 4, context: html, text, full: html, text
• fixing the help message and the tester in hgBeacon.
  
  • src/hg/hgBeacon/README.txt - lines changed 13, context: html, text, full: html, text
  • src/hg/hgBeacon/help.txt - lines changed 14, context: html, text, full: html, text
  • src/hg/hgBeacon/hgBeacon - lines changed 28, context: html, text, full: html, text
  • src/hg/hgBeacon/makefile - lines changed 7, context: html, text, full: html, text
  • src/hg/hgBeacon/testBeacon - lines changed 7, context: html, text, full: html, text
• typo in help message
  
  • src/hg/hgBeacon/help.txt - lines changed 1, context: html, text, full: html, text