galt: changes by commit

review to branch (2009-07-15 to 2009-07-21) v211

• typo fix pine to pipe
  • src/hg/encode/hgEncodeSubmit/runforever.sample 1.3 - lines changed: 1, context: html, text, full: html, text
• burned once, trying a helping hack
  • src/utils/cvsTools/cvsup 1.4 - lines changed: 9, context: html, text, full: html, text
• make util to help configure a sandbox with settings like SSL,BAM
  • src/utils/qa/weeklybld/configureSandbox.csh 1.1 - lines changed: 48, context: html, text, full: html, text
• add settings profiles for SSL and BAM
  • src/utils/qa/weeklybld/defaultBuildSettings.mk 1.1 - lines changed: 2, context: html, text, full: html, text
  • src/utils/qa/weeklybld/downloadBuildSettings.mk 1.1 - lines changed: 2, context: html, text, full: html, text
• handle sandbox configuration
  • src/utils/qa/weeklybld/coBranch.csh 1.6 - lines changed: 6, context: html, text, full: html, text
  • src/utils/qa/weeklybld/makeUserApps.csh 1.3 - lines changed: 4, context: html, text, full: html, text
• adding ./ for users without . on path
  • src/hg/encode/hgEncodeSubmit/go.sample 1.5 - lines changed: 1, context: html, text, full: html, text
• cvscheck checks for sandbox changes without updating the sandbox
  • src/utils/cvsTools/cvscheck 1.1 - lines changed: 2, context: html, text, full: html, text
  • src/utils/cvsTools/cvsup 1.5 - lines changed: 2, context: html, text, full: html, text
  • src/utils/cvsTools/makefile 1.4 - lines changed: 1, context: html, text, full: html, text
• New improved background runner with greater concurrency, throttles on validation and loading, nice-ing of process priorities, fork/exec/zombie-handling, some logging for high server load or high number of processes, some admin functions to display or reset the running-lists
  • src/hg/encode/hgEncodeSubmit/app/controllers/pipeline_controller.rb 1.90 - lines changed: 21, context: html, text, full: html, text
  • src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb 1.15 - lines changed: 31, context: html, text, full: html, text
  • src/hg/encode/hgEncodeSubmit/pipeline_runner.rb 1.3 - lines changed: 215, context: html, text, full: html, text
• resurrecting the progress bar for uploads
  • src/hg/encode/hgEncodeSubmit/app/controllers/pipeline_controller.rb 1.91 - lines changed: 5, context: html, text, full: html, text
  • src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb 1.16 - lines changed: 2, context: html, text, full: html, text