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It finally worked. Thanks everyone.

S.Lee bioinformatics at hanmail.net
Wed Dec 4 00:25:41 EST 2002


I changed a line in the perl script (above thread) where it writes out a
shell script as follows, and it worked!
($GCGFILE versus GCGFILE was my typo that I made when I was typing for
posting).

<from>
print GCGFILE "#!/bin/tcsh\n";

<to>
print GCGFILE "#!/bin/csh\n";

which seems weird because echo $SHELL at the web server machine gives me
"tcsh".

Thanks everyone!

"S.Lee" <bioinformatics at hanmail.net> wrote in message
news:3dec0782$1_5 at corp-goliath.newsgroups.com...
> Thank you very much, Rick.
>
> I tried your code snippet and it worked great in initializing GCG
> environment when run FROM THE SHELL.
>
> 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).
>
> Thanks!
>
> ------------------------------------------------------------
> #!/usr/sbin/perl
>
> print "Content-type: text/html\n";
> print "\n";
>
> $execstr = "/usr/users/gcg/gcgbin/execute/tofasta
> SP_BA:Q93J69 -OUTfile=/SOME_DIRECTORY/out.tfa -default";
>
> $tmpname = "tmpdir.gcgtmp";
> open (GCGFILE,">$tmpname");
> print $GCGFILE "#!/bin/tcsh\n";
> print $GCGFILE "source /usr/gcg/gcgstartup\n";
> print $GCGFILE "gcg\n";
> print $GCGFILE "$execstr\n";
> close $GCGFILE;
> chmod 0770, $tmpname;
> system($tmpname);
>
> ------------------------------------------------------------------
>
> "Rick Westerman" <westerman at purdue.edu> wrote in message
> news:3DEBD7FF.4040705 at purdue.edu...
> > My pipeline code uses a temporary file:
> >
> > my $tmpname = "$tmpdir.gcgtmp";
> >
> > if ($GCGFILE->open (">$tmpname"))
> >         {
> >         print $GCGFILE "#!/bin/csh\n";
> >         print $GCGFILE "source /usr/gcg/gcgstartup\n";
> >         print $GCGFILE "gcg\n";
> >         print $GCGFILE "$execstr\n";
> >         close $GCGFILE;
> >         chmod 0770, $tmpname;
> >         system($tmpname);
> >         }
> >
> > This causes a bunch of initialization code to start up and does not trap
> > for errors (all right in my apps) however it does work.
> >
> > S.Lee wrote:
> >
> > >I have a Perl script that calls a gcg program (tofasta), and runs well
at
> > >UNIX shell.
> > >
> > >A code snippet is, for example, as follows.
> > >
> > >system("/usr/users/gcg/gcgbin/execute/tofasta SP_BA:Q93J69 -default");
> > >
> > >Then, I needed to create an on-line resource, so I converted that Perl
> > >script into a CGI script and executed on-line.
> > >
> > >Now, I cannot execute the gcg tofasta program with the CGI script; It
> simply
> > >does not run. I can guess that the reason is related to gcg
> initialization
> > >and environment (As you know, typing gcg at the command prompt
> initializes
> > >your environment and gives you access to gcg programs. But CGI script
> cannot
> > >do that).
> > >
> > >Does anyone know how to execute a CGI script that calls a gcg program?
> > >
> > >Thanks in advance.
> > >
> > >
> > >
> > >
> > >
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> >
>
>
>
>
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