Executing system command from a CGI script

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Executing system command from a CGI script

Postby biovijay89 » 26. September 2012 12:43

Dear All,

I am trying to run a standalone blast through a Perl CGI script. Please can someone let me know how I could use the system command to execute the blast program.

for instance

system("blastn -query in.fa -db nr -out out.fasta");

The above code works perfectly when I run the perl script locally, but I face an error when I run it from a web server, which says

"blastn -unrecognized external or internal command"

Your inputs are highly appreciated.

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Re: Executing system command from a CGI script

Postby JonB » 03. December 2012 01:48

you probably need an absolute (full) path to the executable, include the file extension to be safe.
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