Commits for max

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

• adding missing file
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.netMhcPan.ra - lines changed 543, context: html, text, full: html, text
• changed gbib internal filenames to make reduce gbib size
  • src/hg/htdocs/goldenPath/help/gbib.html - lines changed 3, context: html, text, full: html, text
• typo in last commit
  • src/hg/htdocs/goldenPath/help/gbib.html - lines changed 1, context: html, text, full: html, text
• removed my useless function again after code review, refs #14118
  • src/hg/lib/fileUi.c - lines changed 13, context: html, text, full: html, text
• fixes to netMhcII track
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.netMhcPanII.ra - lines changed 19, context: html, text, full: html, text
• adding a hg.conf option "isGbib", after gbib meeting
  • src/hg/lib/hdb.c - lines changed 3, context: html, text, full: html, text
• refuse to run hgNear on gbib
  • src/hg/near/hgNear/hgNear.c - lines changed 7, context: html, text, full: html, text
• fixing typos in last commit
  • src/hg/near/hgNear/hgNear.c - lines changed 1, context: html, text, full: html, text
• removing tableList syncing from hgMirror on gbib, as it's not on hgdownload
  • src/hg/hgMirror/hgMirror - lines changed 2, context: html, text, full: html, text
• fixes to netmhc track, after email from david
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.netMhcPanII.ra - lines changed 197, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra - lines changed 1, context: html, text, full: html, text
• changing all gbib command line commands to be prefixed with gbib*.Adding a new command gbibMirrorOff.
  
  • src/hg/htdocs/goldenPath/help/gbib.html - lines changed 10, context: html, text, full: html, text
• various changes to gbib config files
  • src/browserbox/etc/dhcp/dhclient.conf - lines changed 62, context: html, text, full: html, text
  • src/browserbox/etc/issue - lines changed 4, context: html, text, full: html, text
  • src/browserbox/etc/sudoers.d/browserbox - lines changed 3, context: html, text, full: html, text
  • src/browserbox/home/browser/.bashrc - lines changed 45, context: html, text, full: html, text
  • src/browserbox/home/browser/gbibAddTools - lines changed 3, context: html, text, full: html, text
  • src/browserbox/home/browser/updateBrowser - lines changed 1, context: html, text, full: html, text
  • src/browserbox/root/updateBrowser - lines changed 2, context: html, text, full: html, text
  • src/browserbox/root/updateBrowser.sh - lines changed 179, context: html, text, full: html, text
  • src/browserbox/usr/local/apache/cgi-bin/hg.conf - lines changed 9, context: html, text, full: html, text
  • src/browserbox/usr/local/apache/cgi-bin/hg.conf.local - lines changed 2, context: html, text, full: html, text
  • src/browserbox/usr/local/apache/cgi-bin/hgNear - lines changed 19, context: html, text, full: html, text
  • src/browserbox/usr/local/apache/htdocs/images/title.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• adding reference to putty for windows to gbib manual
  • src/hg/htdocs/goldenPath/help/gbib.html - lines changed 3, context: html, text, full: html, text
• fixing typo in gbib manual
  • src/hg/htdocs/goldenPath/help/gbib.html - lines changed 1, context: html, text, full: html, text
• allow both alpha and beta binaries to run on gbib
  • src/hg/lib/web.c - lines changed 9, 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.
  
  • src/hg/hgMirror/hgMirror - lines changed 376, context: html, text, full: html, text
• more config file changes for gbib
  • src/browserbox/etc/dhcp/dhclient.conf - lines changed 62, context: html, text, full: html, text
  • src/browserbox/etc/sudoers.d/browserbox - lines changed 2, context: html, text, full: html, text
  • src/browserbox/home/browser/.bashrc - lines changed 5, context: html, text, full: html, text
  • src/browserbox/root/changes.txt - lines changed 18, context: html, text, full: html, text
  • src/browserbox/root/hg.conf.offline - lines changed 437, context: html, text, full: html, text
  • src/browserbox/root/updateBrowser.sh - lines changed 101, context: html, text, full: html, text
  • src/browserbox/var/spool/cron/crontabs/root - lines changed 12, context: html, text, full: html, text
• fixing broken show subtracks button in hgMirror, refs #14067
  • src/hg/hgMirror/hgMirror - lines changed 48, 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/hgMirror/hgMirror - lines changed 9, context: html, text, full: html, text