[NORDNS] [Bioperl-l] SOAP and bioperl

[Al Park]

Brian,

For example it would be iep.  I understand that there are various methods of entering sequence files into the different tools via -sequencea or -sequence or -seqall, etc depending on the tool itself.

-Al

-----Original Message-----
From: Brian Osborne [mailto:brian_osborne at cognia.com]
Sent: Monday, September 15, 2003 10:41 AM
To: Al Park; bioperl-l at portal.open-bio.org
Subject: RE: [NORDNS] [Bioperl-l] SOAP and bioperl


Al,

What is the value of $program in your code?

Brian O.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Al Park
Sent: Monday, September 15, 2003 9:48 AM
To: bioperl-l at portal.open-bio.org
Subject: [NORDNS] [Bioperl-l] SOAP and bioperl

Hello everyone,

I have encountered a problem using SOAP::Lite and bioperl and I was
wondering if anyone knew of a solution.
My SOAP client calls a perl module which executes the run method in the
Factory::EMBOSS module.  The error that the client generates is: Can't call
method "run" on an undefined variable at xxx where the undefined variable is
$app.

I use the following in my module being called by the SOAP client:

my $factory = Bio::Factory::EMBOSS -> new();
my $app = $factory->program($program);
$app->run({ '-sequencea' => $seq_to_test,
              '-graph' => 'none',
              '-outfile' => $outfile});

Anyone have a solution, tell me what I'm doing wrong, or can just point me
in a direction?
Thanks in advance!

-Al Park

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