Make your own virtual space: Difference between revisions

From genomewiki
Jump to navigationJump to search
m (→‎Keep it current:: adjusted for git)
(Replacing page with 'This page is no longer maintained.')
 
(One intermediate revision by one other user not shown)
Line 1: Line 1:
===So you want to have your own copies of the binaries and your own hgwdev-user.cse.ucsc.edu browser?  Here is a walkthrough:===
This page is no longer maintained.
 
 
====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.xx.yyy>
  ServerName hgwdev-myusername.cse.ucsc.edu
  ServerAlias hgwdev-myusername
  ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-myusername/"
</VirtualHost>
 
 
====Populate my /usr/local/apache/cgi-bin-myusername/ directory for the first time by doing the following:====
 
From my home directory on hgwdev /cluster/home/myusername I type the following things:
 
[myusername@hgwdev ~]$cd kent
[myusername@hgwdev ~/kent]$ cvsup
[myusername@hgwdev ~/kent]$ cd src
[myusername@hgwdev src]$ make libs
[myusername@hgwdev src]$ cd hg
[myusername@hgwdev hg]$ make cgi
[myusername@hgwdev hg]$ cd makeDb/trackDb
[myusername@hgwdev trackDb]$ make update
 
I now have my own compiled version of the cgis.
 
Please note, in order for your browser to be fully functional, there needs to be a symlink to trash and to the javascript in your htdocs-myusername:
 
[myusername@hgwdev ~]$ cd /usr/local/apache/htdocs-myusername
[myusername@hgwdev htdocs-myusername]$ ln -s ../trash
[myusername@hgwdev htdocs-myusername]$ cd js
[myusername@hgwdev js]$ ln -s ../../htdocs/js/myusername
 
==== Create /usr/local/apache/cgi-bin-myusername/hg.conf:====
* create a hg.conf file with these lines using your user name:
include ../cgi-bin/hg.conf
db.trackDb=trackDb_myusername
<span style="color: gray"># Angie recommends that you do <B>not</B> add these lines unless you are using
# your own central database instead of hgcentraltest.
# Assuming you are using the default central.db (hgcentraltest):
# * If you use the default central.* settings from ../cgi-bin/hg.conf, then you can
#  seamlessly switch between genome-test and hgwdev-$USER -- your cookie session
#  will be the same on both.
# * If you change the central.* options, you will have separate cookies between
#  genome-test and hgwdev-$USER, which means your settings from one won't carry
#  over to the other unless you use the same hgsid when switching hosts.
central.host=localhost
central.domain=hgwdev-myusername.cse.ucsc.edu
central.cookie=hguid.hgwdev-myusername
backupcentral.domain=hgwdev-myusername.ucsc.edu </span>
* you can define your own background image by putting it in ~/public_html/ and adding
browser.background=http://hgwdev.cse.ucsc.edu/~myusername/yourimage.jpg 
* here is a generic [[http://hgwdev.cse.ucsc.edu/images/floret.jpg background image]] file you can download and edit.
 
====Keep it current:====
 
Here is a script (makeBinaries.csh) that you can copy and paste into your ~myusername/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
git pull | mail -s 'CVS update report on kent tree' $USER
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:
<PRE>
42 04 * * 1-5 bin/makeBinaries.csh
</PRE>
 
See also: '<B>man 5 crontab</B>' for a description of the fields used
in these crontab lines.
 
When your crontab file is set correctly, hand it off to the cron
system with the command:
<PRE>
$ crontab <yourCrontabFile>
</PRE>
 
Example: '<B>crontab hgwdev.cron</B>'
 
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:
<PRE>
$ crontab -l
</PRE>
 
Cron job tips:  It is better to <B>not</B> 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.
 
 
 
[[Category:Browser Development]]
[[Category:Browser QA]]

Latest revision as of 19:15, 10 March 2011

This page is no longer maintained.