File Changes for jcasper

v336_preview to v336_preview2 (2016-07-11 to 2016-07-18) v336

• confs/hgwbeta.hg.conf
  • lines changed 3, context: html, text, full: html, text
    3dce1c721fb9a027f06564830bc1f4c2d2fe6b65 Sun Jul 17 01:12:15 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• confs/hgwdev.hg.conf
  • lines changed 6, context: html, text, full: html, text
    3dce1c721fb9a027f06564830bc1f4c2d2fe6b65 Sun Jul 17 01:12:15 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• confs/rr.hg.conf
  • lines changed 2, context: html, text, full: html, text
    3dce1c721fb9a027f06564830bc1f4c2d2fe6b65 Sun Jul 17 01:12:15 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 23, context: html, text, full: html, text
    d89c874346552fbb921d6a1d038a79605f6ce613 Wed Jul 13 11:45:07 2016 -0700
    DECIPHER pipeline now runs on their new file format. Also added more data to the hgc output. refs #14465
    
• src/hg/hgc/hgc.c
  • lines changed 37, context: html, text, full: html, text
    d89c874346552fbb921d6a1d038a79605f6ce613 Wed Jul 13 11:45:07 2016 -0700
    DECIPHER pipeline now runs on their new file format. Also added more data to the hgc output. refs #14465
    
• src/hg/htdocs/makefile
  • lines changed 1, context: html, text, full: html, text
    324c1151dbc0092a3960c64add9213743afc66d6 Wed Jul 13 12:07:09 2016 -0700
    Initial stab at having htdocs makefile also run pandoc, refs #14399
    
• src/hg/lib/decipherRaw.sql
  • lines changed 6, context: html, text, full: html, text
    d89c874346552fbb921d6a1d038a79605f6ce613 Wed Jul 13 11:45:07 2016 -0700
    DECIPHER pipeline now runs on their new file format. Also added more data to the hgc output. refs #14465
    
• src/hg/utils/otto/decipher/buildDecipher
  • lines changed 1, context: html, text, full: html, text
    d89c874346552fbb921d6a1d038a79605f6ce613 Wed Jul 13 11:45:07 2016 -0700
    DECIPHER pipeline now runs on their new file format. Also added more data to the hgc output. refs #14465
    
• src/hg/utils/otto/decipher/checkDecipher.sh
  • lines changed 2, context: html, text, full: html, text
    d89c874346552fbb921d6a1d038a79605f6ce613 Wed Jul 13 11:45:07 2016 -0700
    DECIPHER pipeline now runs on their new file format. Also added more data to the hgc output. refs #14465
    
• src/hg/utils/otto/decipher/login.perl
  • lines changed 1, context: html, text, full: html, text
    d89c874346552fbb921d6a1d038a79605f6ce613 Wed Jul 13 11:45:07 2016 -0700
    DECIPHER pipeline now runs on their new file format. Also added more data to the hgc output. refs #14465
    
• src/product/installer/makefile
  • lines changed 17, context: html, text, full: html, text
    324c1151dbc0092a3960c64add9213743afc66d6 Wed Jul 13 12:07:09 2016 -0700
    Initial stab at having htdocs makefile also run pandoc, refs #14399
    
• src/utils/newProg/newProg.c
  • lines changed 1, context: html, text, full: html, text
    5903bc9d1be545a1cc9e1cdf1875ef452c9ca9fb Fri Jul 15 09:52:52 2016 -0700
    Need to set up udc before calling cartEmptyShell, otherwise hubs don't work right, refs #17686
    
  • lines changed 16, context: html, text, full: html, text
    a8fbc07ba5a7a0b99f9b736ecf4a4d1a79d8c6ae Fri Jul 15 17:09:39 2016 -0700
    Additional changes to newProg requested by Angie: set up udcTimeout, knetUdc, and initialize genbank, refs #17686