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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:===
| | This page is no longer maintained. |
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| ====Request a "virtual space" from the cluster-admins:====
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| This includes, among other things, adding a block to the file /usr/local/apache/conf/httpd.conf | |
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| <VirtualHost 128.114.xx.yyy>
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| ServerName hgwdev-myusername.cse.ucsc.edu
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| ServerAlias hgwdev-myusername
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| ScriptAlias /cgi-bin/ "/usr/local/apache/cgi-bin-myusername/"
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| </VirtualHost>
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| ====Populate my /usr/local/apache/cgi-bin-myusername/ directory for the first time by doing the following:====
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| From my home directory on hgwdev /cluster/home/myusername I type the following things:
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| [myusername@hgwdev ~]$cd kent
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| [myusername@hgwdev ~/kent]$ cvsup
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| [myusername@hgwdev ~/kent]$ cd src
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| [myusername@hgwdev src]$ make libs
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| [myusername@hgwdev src]$ cd hg
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| [myusername@hgwdev hg]$ make cgi
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| [myusername@hgwdev hg]$ cd makeDb/trackDb
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| [myusername@hgwdev trackDb]$ make update
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| I now have my own compiled version of the cgis.
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| 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:
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| [myusername@hgwdev ~]$ cd /usr/local/apache/htdocs-myusername
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| [myusername@hgwdev htdocs-myusername]$ ln -s ../trash
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| [myusername@hgwdev htdocs-myusername]$ cd js
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| [myusername@hgwdev js]$ ln -s ../../htdocs/js/myusername
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| ==== Create /usr/local/apache/cgi-bin-myusername/hg.conf:====
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| * create a hg.conf file in '/usr/local/apache/cgi-bin-username/' with these lines using your user name:
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| include ../cgi-bin/hg.conf
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| db.trackDb=trackDb_myusername
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|
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| <span style="color: gray"># Angie recommends that you do <B>not</B> add these lines unless you are using
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| # your own central database instead of hgcentraltest.
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| # Assuming you are using the default central.db (hgcentraltest):
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| # * If you use the default central.* settings from ../cgi-bin/hg.conf, then you can
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| # seamlessly switch between genome-test and hgwdev-$USER -- your cookie session
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| # will be the same on both.
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| # * If you change the central.* options, you will have separate cookies between
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| # genome-test and hgwdev-$USER, which means your settings from one won't carry
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| # over to the other unless you use the same hgsid when switching hosts.
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| central.host=localhost
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| central.domain=hgwdev-myusername.cse.ucsc.edu
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| central.cookie=hguid.hgwdev-myusername
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| backupcentral.domain=hgwdev-myusername.ucsc.edu </span>
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| * you can define your own background image by putting it in ~/public_html/ and adding
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| browser.background=http://hgwdev.cse.ucsc.edu/~myusername/yourimage.jpg
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| * here is a generic [[http://hgwdev.cse.ucsc.edu/images/floret.jpg background image]] file you can download and edit.
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| ====Keep it current:====
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| Here is a script (makeBinaries.csh) that you can copy and paste into your ~myusername/bin directory to make your binaries every night:
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| #!/bin/tcsh
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| if ($HOST != hgwdev) then
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| echo "\n this must be run from hgwdev!\n"
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| endif
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|
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| cd ~/kent/src
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| make clean > /dev/null
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| cd ~/kent
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| git pull | mail -s 'CVS update report on kent tree' $USER
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| cd ~/kent/src
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| make libs
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| cd ~/kent/src/hg
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| make cgi
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| cd ~/kent/src/hg/makeDb/trackDb
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| make update
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| ====Automate it:====
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| Create a crontab file. Note that you may have numerous crontab
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| files. Each machine that you want cron jobs running on will need
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| its own crontab file (assuming the jobs are different). Example,
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| name your crontab file: hgwdev.cron for your hgwdev crontab.
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| With your editor, add a line to your crontab file to run the
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| command at the time you desire. For example, to run your daily
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| build at 04:42 every weekday, the line would read:
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| <PRE>
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| 42 04 * * 1-5 bin/makeBinaries.csh
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| </PRE>
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| See also: '<B>man 5 crontab</B>' for a description of the fields used
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| in these crontab lines.
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| When your crontab file is set correctly, hand it off to the cron
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| system with the command:
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| <PRE>
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| $ crontab <yourCrontabFile>
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| </PRE>
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| Example: '<B>crontab hgwdev.cron</B>'
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| To see what you have submitted to the cron system, ask it to
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| display what it knows about your cron jobs with the -l argument:
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| <PRE>
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| $ crontab -l
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| </PRE>
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| Cron job tips: It is better to <B>not</B> run your jobs exactly at
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| the top of the hour. They would be competing with system cron jobs that
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| are running at times like the top of the hour. Better to run your job
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| at odd minutes during the hour. Don't use the example time listed here,
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| otherwise everyone's job will be running at 04:42 every day and competing
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| with each other.
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| Any output to stdout or stderr by your cron job will be emailed to you
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| via the cron system as it runs your job. If you would rather not
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| see that output in email, construct your cron job shell script in such
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| a way that it takes care of all of its stdout and stderr output. For
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| example, it could create an organized by date hierarchy of log files
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| for its output.
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| [[Category:Browser Development]]
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| [[Category:Browser QA]]
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