September 26th, 2012, 07:13 AM
Executing system command from a CGI script
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.
September 26th, 2012, 10:23 AM
Specify the full path to blastn in the system call.
September 27th, 2012, 12:20 AM
I tried the below code. but this time it says "premature end of script headers".
Originally Posted by FishMonger
$blast = "C:\\Apache24\\htdocs\\blast\\blastn -version";
I tried putting in the exe file into the apache folder itself, but still no luck. Please can you advise me further.
September 27th, 2012, 09:31 AM