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.
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.