Blastall run from CGI script

Jonathan Epstein Jonathan_Epstein at nih.gov
Fri Sep 15 12:21:52 EST 2000


In addition to Tim's excellent suggestions, you should also consider
setting the "NCBI" environment variable in your Perl program to point to
the directory which contains the .ncbirc file.

- Jonathan


andrew_walsh at my-deja.com wrote:
> 
> Hi everyone,
> 
> I'm a newbie to the usenet community so please excuse my format,
> syntax...
> 
> I've been trying to run blastall from a CGI script on a Linux (RH 6.2)
> machine.  The blastall program and Apache web server are on the same
> machine.  I can run the program via perl scripts from the command line
> without problem.  But when I create the cgi script and execute it from
> the web page I get the same error message in my httpd error_log file-
> [blastall] WARNING: could not find index files...
> 
> I've already used formatdb to create these index files.  The correct
> path is given in the CGI script.  My webserver (user, group: http) owns
> all of these files.  All of these files are in the home directory of
> http (not httpd).
> 
> The .ncbirc file has been created with appropriate paths for Data and
> BLASTDB.  This file has been put in what I can imagine would be every
> possibly relevant directory (dir containing blastall, cgi-bin dir, http
> home dir).
> 
> I'm using the Open2 module to open a file handle for the blastall
> program and sending sequence from a file as input.  Then I have the
> results sent as standard output back to the web page.
> 
> I just get the header for the Blast result and then query length (this
> isn't even right since it says 15 letters, not the actual length of the
> sequence in the file referened in the cgi script).  I could well be
> wrong, but I don't think that the problem is my relative newbie status
> in cgi- I can get echo to send STDOUT to the web page.
> 
> If anyone has any ideas on what I'm doing wrong or overlooking they
> would be greatly appreciated.
> THANKS!!
> 
> Andrew
> 
> Sent via Deja.com http://www.deja.com/
> Before you buy.







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