Restart-BBS-HOWTO.TXT

Before restarting the BBS run script on a given node:

 1. Confirm that if restarted, there is enough time for the run script to 
    complete before the postrun script starts.

 2. Make sure the run script is not currently running and that no one else is
    logged in as the 'biocbuild' user.
 
        ps -u biocbuild
        ps auxwww | grep biocbuild

 3. On Linux and Mac do a  `kill -9 -1` as the 'biocbuild' user to 
    git rid of any leftover processes. This will kick you off the machine if 
    you were logged in as 'biocbuild' and will terminate the sessions of 
    anyone else logged on the machine as 'biocbuild'.

    The `kill` command also has the advantage of terminating any rogue child 
    processes started by the BBS. In the past we've hit a bug where if
    a package has a timeout, "R CMD build" or "R CMD check" processes
    are not killed by the BBS and they keep running in the background
    forever. We haven't seen this problem for awhile so the bug may be fixed.

 4. Remove R library lock dir (BBS_R_HOME/library/00LOCK) if present.

 5. On Windows, clean BBS_WORK_TOPDIR/tmp/ and BBS_WORK_TOPDIR/tmpdir/.

 6. You can also remove the current log file (should be in 
    BBS_WORK_TOPDIR/log/) if you don't want to keep the output of the
    previous runs.

Then restart the run:

 1. Make the appropriate change in the crontab (Unix) or in the Task Scheduler
    (Windows) to have BBS automatically restarted in the next minutes.

 2. If you want to restart the run by hand (instead of using the crontab
    or the Task Scheduler) do the following (as 'biocbuild'):
    - On malbec1:
        cd /home/biocbuild/BBS/3.6/bioc/malbec1 
        ./run.sh >>/home/biocbuild/bbs-3.6-bioc/log/malbec1-`date +\%Y\%m\%d`-run.log 2>&1'

    - On tokay1:
        cd C:\Users\biocbuild\BBS\3.6\bioc\tokay1
        run.bat >> C:\Users\biocbuild\bbs-3.6-bioc\log\tokay1.log 2>&1

    - should be easy to adapt the above commands on other nodes...