Thanks Michael,
The error was as bellow in error_log file:
Can't exec "/home/soumya/Application/BLAST/blastall":
Permission denied at
/var/www/cgi-bin/bic_genscan/file3.cgi line 19.
Now I've copied the program blastall into the same
directory so that the user running apache can have the
accesibility. Thanks, it is running fine in localhost.
Now I want to send the request from my system to our
server (i.e. in Sun solaris).
If I don't write the system command in my cgi file
then it works fine. And if I write the system command
in my cgi file with only program name it send me back
the list of options those are required to run the
program, but as I write the options it ends with the
following error flushed on my machine:
"500 Internal Server Error".
And in /usr/local/apache/logs/error_log file :
[Wed Mar 26 13:47:45 2003] [error] [client
203.90.127.104] malformed header
from script. Bad header=BLASTN 2.2.4 [Aug-26-2002]:
/usr/local/apache/cgi-bin/local/file3.cgi
Please suggest me what might be the error.
If there is any way to run blastall from its original
directory rather copying it to the desired path.
As user soumya(i.e. myself) loged in and running this
program, what I belive user soumya is running the
apache, if not, who else is running the apache (for
information there is a user apache is also there in my
system) how to know that?
regards,
Soumyadeep
--- Michael Weber <[EMAIL PROTECTED]> wrote:
> Does the user running Apache have rights to the
> /home/soumya/Application/BLAST/blastall file and the
> data directories?
>
> What's in the access_log or error_log when you run
> the script from the
> web page?
>
> -Michael
>
> >>> Soumyadeep nandi <[EMAIL PROTECTED]>
> 03/25/03 07:39AM >>>
> Hi,
>
> I am stuck with another problem. I want to send a
> request from the perl file to the server. The server
> receives the request with a cgi file which will
> process the request by executing a system command
> and
> send back the result. But my cgi script is not
> executing the system command.
>
> The cgi script I wrote as file3.cgi as bellow:
> #!/usr/bin/perl -w
>
> use CGI;
>
> print "Content-type:text/plain\n\n";
>
> $query = new CGI;
>
> print "blast\n";
>
> $str = $query->param('st');
>
> print "here the string is : $str\n";
>
> system("/home/soumya/Application/BLAST/blastall
> -p
> blastn -d
> /home/soumya/Application/BLAST/data/ecoli.nt
> -i /var/www/cgi-bin/bic_genscan/testseq -o
> /var/www/cgi-bin/bic_genscan/testblastout");
> -------------------------
>
> This command in the above script is calling another
> program(blastall) residing in
> /home/soumya/Application/BLAST, and -p,
> -d, -i and -o are the arguments required as a
> parameter to run the program.
> This command should create a file (testblastout) in
> the directory(/var/www/cgi-bin/bic_genscan), as I've
> passed the name as the argument (-o
> /var/www/cgi-bin/bic_genscan/testblastout) in the
> command.
> But it is not creating any file there. Then I wrote
> a
> perl script so that the job could be done.
>
> The perl script is as perl1.pl as bellow:
> #!/usr/bin/perl
>
> $str = shift;
> chomp = $str;
>
> print "received the sequence\n";
> system("/home/soumya/Application/BLAST/blastall -p
> blastn -d
> /home/soumya/Application/BLAST/data/ecoli.nt
> -i /var/www/cgi-bin/bic_genscan/\"$str\" -o
> /var/www/cgi-bin/bic_genscan/testblastout");
> print "done...\n";
> -----------------------------
>
> And replaced the system... line in cgi file with
> system("./perl1.pl testseq");
> Still it is not executing the system command.
>
> If I run this perl file alone without calling it
> from
> any other file then it executes. (./perl1.pl testseq
> from command line).
>
> What should I do to run the system command either
> from
> cgi or perl file in this above scenario.
>
> As I can not see my earliar mail depicting the same
> problem in the list I am sending it again. I am
> sorry
> if this mail is showing twice.
>
> With regards,
> Soumyadeep
>
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