[GeneX-dev] Re: xcluster_handler.pl and xcluster_form.pl

[Harry M. <man...@ho...>]

Hi there,

(I'm broadcasting this to our dev mailing list as it may be of broader interest.)

You can get both programs with the genex-server package which can be gotten at:

http://genebox.ncgr.org/genex/download/genex-server/GeneX-Server-1.0.3.tar.gz

You can install the whole GeneX system in which case you'll get the database system as well as the analysis tools or if you JUST want xcluster, you can go into the extracted directory:

GeneX-Server-1.0.3

xcluster/
|-- xcluster.form.pl.in    
|-- xcluster.help.html
|-- xcluster.notes
|-- xcluster.test.dataset
`-- xcluster_handler.pl.in

and edit & install them yourself.

the files ending in '.in' are input files that contain variables (%%REPLACE_ME%%) that need to be replaced with variables that define various things about your system.  They should be pretty easy to
figure out:

xcluster.form.pl.in:
%%START_PERL%%
%%HTML_ROOT_URL%% # bare HTML root (often 'http://your.machine.com')
%%XCLUSTER_DIR%%  # combines the genex dir w/ the xcluster dir (often 'genex/xcluster'
                  # but if installing only xcluster, it could be 'xcluster')
%%CGI_ROOT_URL%%  # bare CGI-BIN root as above (often
                  #    'http://your.machine.com/cgi-bin')

xcluster_handler.pl.in:
%%START_PERL%%   [as above]
%%WWWHOST%%           #  the Fully Qualified Domain Name of the host machine
%%CGITMPDIR%%         #  where you want it to stash temp files (often '/tmp/genex')
%%GENEX_HTM_URL%%     #  where you would install genex (often
                      #    'http://your.machine.com/genex')
%%XCLUSTER_DIR%%      #  [as above]
%%HTTP_ERR_LOG%%      #  where your httpd error log is
%%GNUTAIL%%           #  the full path to your GNU 'tail'
%%GNUTAR%%            #  the full path to your GNU 'tar'
%%XCLUSTER%%          #  the full path to the xcluster binary


remove the '.in' suffix from the files, move them to the places you've indicated,
set the permissions appropriately, and try them out.

We are considering making all the analyses a separate module so you can install them without the database as well as with it. 
 
Smita Mitra wrote:
> 
> Dear Harry,
> 
> We have obtained a lisence from Stanford for using
> xcluster. We would like to use your
> xcluster_handler.pl and xcluster_form.pl for data
> analysis.
> 
> Would you be able to provide me with these 2 programs
> and some notes on the directory structure you have in
> place with xcluster and the programs xcluster calls.
> This would make the installation of xcluster and its
> integration with a database much easier for us.
> 
> Thanks a lot!
> Regards, Smita.
> 
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-- 
Cheers,
Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...