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How to execute GCG via CGI?

Simon Andrews simon.andrews at bbsrc.ac.uk
Tue Dec 3 04:41:18 EST 2002

"S.Lee" wrote:
> Thank you very much, Rick.
> I tried your code snippet and it worked great in initializing GCG
> environment when run FROM THE SHELL.

The code you posted would not have worked from the shell either so I'm
sure how you judged it to have worked...
> However, it still does not run ON THE WEB. It does not produce an output
> file.
> Could you please take a look at my CGI script and let me know what is going
> on? (Of course, I chmod'ed the output directory writable to ugo, so writing
> privilege issue cannot be the reason).

I think a bit of error checking is in order.  A modified and commented
of your code is below.

Hope this helps


# Always put on your safety belt!

use warnings; # Add -w to the first line if using perl <5.6
use strict;

# For convenience let's look at our errors in
# the browser

use CGI::Carp qw(fatalsToBrowser);
my $execstr = "/usr/users/gcg/gcgbin/execute/tofasta
SP_BA:Q93J69 -OUTfile=/SOME_DIRECTORY/out.tfa -default";
my $tmpname = "tmpdir.gcgtmp";

# Where do you think this file will be created?  Many
# web servers will have a very different idea about the
# current working directory than you have!

chdir('/somewhere_my_web_server_can_write_to/') || die "Can't chdir:

open (GCGFILE,">$tmpname") || die "Can't create $tmpname: $!";
#                          ***********************************
# You should always check that an open succeeds

### print $GCGFILE "#!/bin/tcsh\n";
### etc.
# These lines don't do what you think they do.  You are
# trying to print to $GCGFILE, a new variable you have just
# created, rather than printing to GCGFILE, the filehandle 
# you tried to open before.  Use strict would have
# caught the creation of a new variable, but you should have
# seen a warning saying "Can't use an undefined value as a 
# symbol reference" anyway...

source /usr/gcg/gcgstartup


close (GCGFILE) || die "Can't close GCGFILE: $!";

chmod (0700,$tmpname) || die "Can't chmod: $!";

print <<"END_HTML";
Content-type: text/html



print `./$tmpname 2>&1`;

# Here I've executed the command in backticks
# to grab it's output.  I've also redirected
# stderr to stdout so you should see any errors
# which occur

unless (-e '/SOME_DIRECTORY/out.tfa'){
  print "Nope - Something went wrong\n";

print '</pre></body></html>';

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