Make your own virtual space

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So you want to have your own copies of the binaries and your own hgwdev-user.cse.ucsc.edu browser? Here is a walkthrough:

Request a "virtual space" from the cluster-admins:

This includes, among other things, adding a block to the file /usr/local/apache/conf/httpd.conf 

<VirtualHost 128.114.50.189>
 ServerName hgwdev-kayla.cse.ucsc.edu
 ServerAlias hgwdev-kayla
 ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-kayla/"
</VirtualHost>


Populate my /usr/local/apache/cgi-bin-kayla/ directory for the first time by doing the following:

From my home directory on hgwdev /cluster/home/kayla I type the following things: 

[kayla@hgwdev ~]$cd kent
[kayla@hgwdev ~/kent]$ cvsup
[kayla@hgwdev ~/kent]$ cd src
[kayla@hgwdev src]$ make libs
[kayla@hgwdev src]$ cd hg
[kayla@hgwdev hg]$ make cgi
[kayla@hgwdev hg]$ cd makeDb/trackDb
[kayla@hgwdev trackDb]$ make update

I now have my own compiled version of the cgis.


Edit my /usr/local/apache.cgi-bin-kayla/hg.conf:

  • You can copy this file from another user, but make sure to replace their name with your name in the appropriate (4) places.
  • Pay attention to the following lines (they will need to be edited or added):
central.host=localhost
central.domain=hgwdev-kayla.cse.ucsc.edu
central.cookie=hguid.hgwdev-kayla
backupcentral.domain=hgwdev-kayla.ucsc.edu
  • Also play with the line:
browser.background=/images/floret.jpg to change what background your browser displays.
  • here is a generic [image:floret.jpg] file you can download and edit.

Keep it current:

Here is a script (makeBinaries.csh) that you can copy and paste into your ~kayla/bin directory to make your binaries every night: 

#!/bin/tcsh

if ($HOST != hgwdev) then
  echo "\n  this must be run from hgwdev!\n"
endif

cd ~/kent/src
make clean > dev/null
cd ~/kent
/cluster/bin/scripts/cvsup | mail -s 'CVS update report on kent tree' kayla
cd ~/kent/src
make libs
cd ~/kent/src/hg
make cgi
cd ~/kent/src/hg/makeDb/trackDb
make update

Automate it:

Create a crontab file. Note that you may have numerous crontab files. Each machine that you want cron jobs running on will need its own crontab file (assuming the jobs are different). Example, name your crontab file: hgwdev.cron for your hgwdev crontab. With your editor, add a line to your crontab file to run the command at the time you desire. For example, to run your daily build at 04:42 every weekday, the line would read: 

42 04 * * 1-5 bin/dailyBuild.sh

See also: 'man 5 crontab' for a description of the fields used in these crontab lines.

When you crontab file is set correctly, hand it off to the cron system with the command: 

$ crontab <yourCrontabFile>

Example: 'crontab hgwdev.cron'

To see what you have submitted to the cron system, ask it to display what it knows about your cron jobs with the -l argument: 

$ crontab -l

Cron job tips: It is better to not run your jobs exactly at the top of the hour. They would be competing with system cron jobs that are running at times like the top of the hour. Better to run your job at odd minutes during the hour. Don't use the example time listed here, otherwise everyone's job will be running at 04:42 every day and competing with each other.

Any output to stdout or stderr by your cron job will be emailed to you via the cron system as it runs your job. If you would rather not see that output in email, construct your cron job shell script in such a way that it takes care of all of its stdout and stderr output. For example, it could create an organized by date hierarchy of log files for its output.

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