File Changes for max

v307_preview2 to v307_base (2014-10-06 to 2014-10-13) v307

• src/browserbox/etc/dhcp/dhclient.conf
  • lines changed 62, context: html, text, full: html, text
    various changes to gbib config files
  • lines changed 62, context: html, text, full: html, text
    more config file changes for gbib
• src/browserbox/etc/issue
  • lines changed 4, context: html, text, full: html, text
    various changes to gbib config files
• src/browserbox/etc/sudoers.d/browserbox
  • lines changed 3, context: html, text, full: html, text
    various changes to gbib config files
  • lines changed 2, context: html, text, full: html, text
    more config file changes for gbib
• src/browserbox/home/browser/.bashrc
  • lines changed 45, context: html, text, full: html, text
    various changes to gbib config files
  • lines changed 5, context: html, text, full: html, text
    more config file changes for gbib
• src/browserbox/home/browser/gbibAddTools
  • lines changed 3, context: html, text, full: html, text
    various changes to gbib config files
• src/browserbox/home/browser/updateBrowser
  • lines changed 1, context: html, text, full: html, text
    various changes to gbib config files
• src/browserbox/root/changes.txt
  • lines changed 18, context: html, text, full: html, text
    more config file changes for gbib
• src/browserbox/root/hg.conf.offline
  • lines changed 437, context: html, text, full: html, text
    more config file changes for gbib
• src/browserbox/root/updateBrowser
  • lines changed 2, context: html, text, full: html, text
    various changes to gbib config files
• src/browserbox/root/updateBrowser.sh
  • lines changed 179, context: html, text, full: html, text
    various changes to gbib config files
  • lines changed 101, context: html, text, full: html, text
    more config file changes for gbib
• src/browserbox/usr/local/apache/cgi-bin/hg.conf
  • lines changed 9, context: html, text, full: html, text
    various changes to gbib config files
• src/browserbox/usr/local/apache/cgi-bin/hg.conf.local
  • lines changed 2, context: html, text, full: html, text
    various changes to gbib config files
• src/browserbox/usr/local/apache/cgi-bin/hgNear
  • lines changed 19, context: html, text, full: html, text
    various changes to gbib config files
• src/browserbox/usr/local/apache/htdocs/images/title.jpg
  • lines changed 0, context: html, text, full: html, text
    various changes to gbib config files
• src/browserbox/var/spool/cron/crontabs/root
  • lines changed 12, context: html, text, full: html, text
    more config file changes for gbib
• src/hg/hgMirror/hgMirror
  • lines changed 2, context: html, text, full: html, text
    removing tableList syncing from hgMirror on gbib, as it's not on hgdownload
  • lines changed 376, context: html, text, full: html, text
    many changes to hgMirror. I am definitely not proud of this script. Codereview is not critical here, as the script runs only on virtual machines
    and not on the RR.
    This commit changes the way gbib does its post-rsync update, it's now in
    the jobscript, not in the main CGI anymore. It stops/starts the mysql
    server before/after updates and does a mysqlcheck after it.
    The postRsyncUpdates iterate over all DBs now and not only hg19.
    Some redundant code was removed from the file size calculation.
    I am now trying to remove outdated and useless ENCODE files from the download, this
    decreased filesize I believe by 500GB in hg19.
    The whole genome selection menu is build differently now.
    most of the track data is now stored in a pickled file for faster
    loading.
    There is a "please wait" message shown while the track data is built.
    Deactivating the "deflate" apache module allows to show the message in
    the browser (even though there still seems to be some stdout buffering going
    on, somewhere)
    Thanks for reading until here.
    
  • lines changed 48, context: html, text, full: html, text
    fixing broken show subtracks button in hgMirror, refs #14067
  • lines changed 9, context: html, text, full: html, text
    adding a list of links to the track groups to hgMirror, there are toomany tracks in hg19 currently to fit onto a screen.
    
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 3, context: html, text, full: html, text
    changed gbib internal filenames to make reduce gbib size
  • lines changed 1, context: html, text, full: html, text
    typo in last commit
  • lines changed 10, context: html, text, full: html, text
    changing all gbib command line commands to be prefixed with gbib*.Adding a new command gbibMirrorOff.
    
  • lines changed 3, context: html, text, full: html, text
    adding reference to putty for windows to gbib manual
  • lines changed 1, context: html, text, full: html, text
    fixing typo in gbib manual
• src/hg/lib/fileUi.c
  • lines changed 13, context: html, text, full: html, text
    removed my useless function again after code review, refs #14118
• src/hg/lib/hdb.c
  • lines changed 3, context: html, text, full: html, text
    adding a hg.conf option "isGbib", after gbib meeting
• src/hg/lib/web.c
  • lines changed 9, context: html, text, full: html, text
    allow both alpha and beta binaries to run on gbib
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.netMhcPan.ra
  • lines changed 543, context: html, text, full: html, text
    adding missing file
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.netMhcPanII.ra
  • lines changed 19, context: html, text, full: html, text
    fixes to netMhcII track
  • lines changed 197, context: html, text, full: html, text
    fixes to netmhc track, after email from david
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    fixes to netmhc track, after email from david
• src/hg/near/hgNear/hgNear.c
  • lines changed 7, context: html, text, full: html, text
    refuse to run hgNear on gbib
  • lines changed 1, context: html, text, full: html, text
    fixing typos in last commit