Commits for max

v299_preview2 to v299_base (2014-04-21 to 2014-04-28) v299

• cosmetic changes to make gbib more distinct from main site and also toremove links that direct user back to main site (unless required, like
  suggestion box), refs #12717
  
  • src/browserbox/README.txt - lines changed 4, context: html, text, full: html, text
  • src/browserbox/root/changes.txt - lines changed 3, context: html, text, full: html, text
  • src/browserbox/root/cleanVm.sh - lines changed 3, context: html, text, full: html, text
  • src/browserbox/root/cronUpdate.sh - lines changed 1, context: html, text, full: html, text
  • src/browserbox/root/mirrorTrack - lines changed 1, context: html, text, full: html, text
  • src/browserbox/root/updateBrowser.sh - lines changed 25, context: html, text, full: html, text
  • src/browserbox/usr/local/apache/htdocs/favicon.ico - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/browserbox/usr/local/apache/htdocs/images/homeIconSprite.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/browserbox/usr/local/apache/htdocs/style/gbib.css - lines changed 3, context: html, text, full: html, text
• adding include file support to hgMirror
  • src/hg/hgMirror/hgMirror - lines changed 25, context: html, text, full: html, text
• compile-time option to add a password to some bigBed files for gbib-onlytracks, refs #11957
  
  • src/hg/hgTracks/bigBedTrack.c - lines changed 6, context: html, text, full: html, text
  • src/inc/common.mk - lines changed 11, context: html, text, full: html, text
• make hg.conf option false by default after comment from Braney
  • src/hg/lib/hdb.c - lines changed 1, context: html, text, full: html, text
• improving some comments in hgMirror
  • src/hg/hgMirror/hgMirror - lines changed 5, context: html, text, full: html, text
• moving cgiApoptosis call to a better place which should work in mostCGIs.
  
  • src/hg/lib/cart.c - lines changed 2, context: html, text, full: html, text
• making hgMirror depend on a flag defined in hg.conf
  • src/hg/hgMirror/hgMirror - lines changed 6, context: html, text, full: html, text
• refactoring some code of hgMirror into a function
  • src/hg/hgMirror/hgMirror - lines changed 17, context: html, text, full: html, text
• adding hgMirror to top-level cgi target, to get it onto hgdownload.thanks to a new hg.conf option, it will not run on the RR.
  
  • src/hg/makefile - lines changed 1, context: html, text, full: html, text
• fixing stupid typo
  • src/hg/hgMirror/hgMirror - lines changed 1, context: html, text, full: html, text
• closing open cursors, hoping this helps against some errors on the box
  • src/hg/hgMirror/hgMirror - lines changed 12, context: html, text, full: html, text
• adding empty "clean" target
  • src/hg/hgMirror/makefile - lines changed 2, context: html, text, full: html, text
• adding browserbox name to cgiApoptosis again, it mysteriously disappeared
  • src/hg/lib/cgiApoptosis.c - lines changed 2, context: html, text, full: html, text
• updating docs to reflect final location of files, refs #11957
  • src/hg/htdocs/goldenPath/help/gbib.html - lines changed 1, context: html, text, full: html, text
• as hgMirror is handling all the post-rsync changes to tables, need toadd a few rows for box-specific tracks on hg19
  
  • src/hg/hgMirror/hgMirror - lines changed 20, context: html, text, full: html, text
• adding section about increasing memory to doc, refs #11957
  • src/hg/htdocs/goldenPath/help/gbib.html - lines changed 9, context: html, text, full: html, text
• fixing small mysqldb and makefile bug
  • src/hg/hgMirror/hgMirror - lines changed 2, context: html, text, full: html, text
  • src/hg/hgMirror/makefile - lines changed 4, context: html, text, full: html, text
• tMerge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent
• documenting the gbib hg.conf options, in case that mirrors want to usethem. refs #11957
  
  • src/product/ex.hg.conf - lines changed 26, context: html, text, full: html, text