Commits for max

v322_base to v323_preview (2015-09-14 to 2015-09-21) v323

• fixes after code review refs #16013
  
  • src/hg/hgTracks/menu.c - lines changed 1, context: html, text, full: html, text
• making hgTracks copy the extTools.ra file to activate the external tools
  menu. refs #15113
  
  • src/hg/hgTracks/makefile - lines changed 1, context: html, text, full: html, text
• adding menu entries under genomes and genome browser, refs #16022
  
  • src/hg/hgTracks/hgTracks.c - lines changed 13, context: html, text, full: html, text
  • src/hg/htdocs/inc/globalNavBar.inc - lines changed 17, context: html, text, full: html, text
  • src/hg/htdocs/style/nice_menu.css - lines changed 6, context: html, text, full: html, text
  • src/hg/js/jquery.plugins.js - lines changed 1, context: html, text, full: html, text
• adding a link to the share data folder in gbib, refs #16022
  
  • src/browserbox/root/updateBrowser.sh - lines changed 2, context: html, text, full: html, text
• allow loading of local files in gbib without the udc cache, refs #16022
  
  • src/browserbox/usr/local/apache/cgi-bin/hg.conf - lines changed 6, context: html, text, full: html, text
• fixing url in gbib readme
  
  • src/browserbox/README.txt - lines changed 1, context: html, text, full: html, text
• allowing auto-creating of track line from local files, refs #16011
  
  • src/hg/lib/customPp.c - lines changed 2, context: html, text, full: html, text
• fixing one letter typo
  
  • src/browserbox/root/updateBrowser.sh - lines changed 1, context: html, text, full: html, text
• adding a variable CGI-BIN_DEST that is either CGI-BIN_USER or
  CGI-BIN_BETA or CGI-BIN, depending on how make was called.
  This should avoid the triplicated rules we have everywhere.
  It doesn't work when one wants to run "make alpha beta my" but
  I think we never do that.
  Using this to copy an .ra file to the cgi-bin directory. refs #15113
  
  • src/hg/hgTracks/makefile - lines changed 1, context: html, text, full: html, text
  • src/inc/cgi_build_rules.mk - lines changed 15, context: html, text, full: html, text
• libifying cartGetPosition because this code is needed twice, once in
  hgTracks and also in cart.c for setting the page title. refs #16022,
  note 18
  
  • src/hg/hgTracks/hgTracks.c - lines changed 20, context: html, text, full: html, text
  • src/hg/inc/cart.h - lines changed 10, context: html, text, full: html, text
  • src/hg/lib/cart.c - lines changed 43, context: html, text, full: html, text
• fixing split table bug in hgMirror, refs #16033
  
  • src/hg/hgMirror/hgMirror - lines changed 14, context: html, text, full: html, text
• oops, forgot the tables all_mrna and all_est. refs #16033
  
  • src/hg/hgMirror/hgMirror - lines changed 6, context: html, text, full: html, text
• wording change of ext tools menu
  
  • src/hg/hgTracks/extTools.ra - lines changed 2, context: html, text, full: html, text
• Revert "adding menu entries under genomes and genome browser, refs #16022"
  
  This reverts commit 385f6d8b1f19463d2103cee18970fa833411293f.
  
  Conflicts:
  src/hg/hgTracks/hgTracks.c
  
  • src/hg/hgTracks/hgTracks.c - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/inc/globalNavBar.inc - lines changed 17, context: html, text, full: html, text
  • src/hg/htdocs/style/nice_menu.css - lines changed 6, context: html, text, full: html, text
  • src/hg/js/jquery.plugins.js - lines changed 1, context: html, text, full: html, text
• fixing merge conflict overlooked in last commit
  
  • src/hg/hgTracks/hgTracks.c - lines changed 3, context: html, text, full: html, text