SNPscan README file

SNPscan is a web-based service. To install a local version of the SNPscan 
server, you may need to adjust some defaults within the SNPscan.pl and 
SNPscan.R codes to make it work under your local environment. This local 
version will allow you to generate the plots and tables, up to the file size 
you sepcified, which is the majority of the work. It is not intended to be
an exact copy of the web version, to keep it simple.

First, the outline of the design of SNPscan server:

1. The web page on the user side sends into to SNPscan.pl via Apache's 
   POST method.
2. SNPscan.pl, running on the SNPscan server side, substitutes user's options
   in the SNPscan.R code with user's selections.
3. SNPscan.pl make a system call to run the generated R codes
4. The R codes produce a temporary PostScript output in a temporary directory.
5. The SNPscan.pl then reads in the PostScript file; uses it to generate
   PNG, TIF and PDF files; and moves all four files to another directory
   accesssible by the web user for download.
6. kkisnp.pl provides the KKI SNP Analysis Tools, linked with SNPscan

Therefore, depending on your web server's setup, you may need to modify the
following:

For the snpscan_index.htm -

* line 48: modify the file path for SNPscan.pl

For SNPscan_titlegraphic.gif -

* put it in the same file directory of snpscan_index.htm

For the SNPscan.pl -

* line 36: modify the "/tmp/SNPscan" to a directory on your system
* line 411: modify the "/usr/local/bin/R" to the location of R installed on
  your system
* between lines 514~547 and line 572: modify all the instances of
  "pevsnerlab.kennedykrieger.org" according to your web server

For the SNPscan.R -

* line 22 and 23: modify the file locations for "chroSize.Build3X" and
  "centromere.Build3X:

  Note: There are two files are based on Build 34, another two based on 
        Build 35. Build 35 is the Build currently used by Affymetrix's 
        Chromosome Copy Number Analysis Tool 3.0. If your data were generated 
        earlier, it's most likly to be based on Build 34.

For the kkisnp.pl -

* line 42: modify the "/tmp/SNPscan" temporary directory
* various places: modify the "pevsnerlab.kennedykriger.org" according to your
  web server


Last Updated:  February 7, 2006