Passing and recieving params

[MonkPaul]

I suppose that is one option.But i have a load of other modules to call from within the BlastTool.cgi script.

I was just trying to do this to try and learn how to execute another script really so i know personally what i am doing in the long run.

Over all i have

ComLine.pm
MergeFiles.pm
parseFiles.pm
Email.pm
Filter.pm
FilterHeader.cgi
runBlast.cgi

I was just trying to get the first script to be an input one, then actually perform the tasks after the input has been gathered.

I have really ballsed up the writing of this code as its currently all in one cgi file with separate functions, so i am in the process of trying to split it all up and get it to work properly from within different modules. Im ok with calling the modules from within the BlastToolcgi, but i just wanted to get the input in a separate script and possibly implement a loading page too.

Argggggggghhhhhhh, what have i done!!

[ikegami]

i have a load of other modules to call from within the BlastTool.cgi script.

So what's the problem? The BlastTool module (formerly BlastTool.cgi) can still load all the modules it wants.

I was just trying to do this to try and learn how to execute another script really so i know personally what i am doing in the long run.

What we're seeing is "I want to wash my cat, so can you teach me how to neuter a cat? I know what I am doing in the long run." This communication problem is making it rather hard to help.

[MonkPaul]

Right, i will start again and take on board what you said.

Im going to leave the BlastTool.cgi as the first port of call, then just split up the modules.

What in effect i need to do, as the finished article, is to wrap the software so that other java applications can input their params and get output back. But still have the capability to produce output to a web browser

Another question then: If i have input from both command line and web page, can i get the input the same way or do i have to use an if statement eg.

  $html = new CGI;  # create a new instance of CGI 
  $seq = $html->param('Sequence_input');
  
  if($seq eq "")
  {
    GetOptions( "sequence=s" => \$seq);
  }

monkPaul.

[ikegami]

The following would be more appropriate:

my $seq;
...

if (defined($ENV{GATEWAY_INTERFACE})) {
   # We were called via CGI.
   my $cgi = new CGI;
   $seq = $cgi->param('Sequence_input');
   ...
}
else
{  
   GetOptions(
      "sequence=s" => \$seq,
      ...
   );
}