Bio-Phylo-CIPRES

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lib/Bio/Phylo/CIPRES.pm  view on Meta::CPAN


Bio::Phylo::CIPRES - Reusable components for CIPRES REST API access

=head1 SYNOPSIS

 my $cipres = Bio::Phylo::CIPRES->new( 
 	'infile'    => 'infile.fasta',                 # input data file
 	'tool'      => 'MAFFT_XSEDE',                  # tool to run
 	'param'     => { 'vparam.runtime_' => 7.5 },   # extra parameters, e.g. max runtime
 	'outfile'   => { 'output.mafft' => 'out.fa' }, # name of output data to fetch
 	'yml'       => 'config.yml',	               # client credentials
 );
 
 my $url = $cipres->run;
 
 $cipres->clean_job( $url );

=head1 DESCRIPTION

The CyberInfrastructure for Phylogenetic RESearch (L<CIPRES|http://www.phylo.org>) is a 
portal that provides access to phylogenetic analyses tools that can be run on the XSEDE

lib/Bio/Phylo/CIPRES.pm  view on Meta::CPAN

=cut

sub ua {
	my $self = shift;
	my $host = URI->new( $self->url )->host();
	my $user = $self->user;
	my $pass = $self->pass;
	my $ua   = LWP::UserAgent->new;
	DEBUG "Instantiating UserAgent $host:$PORT / $REALM / $user:****";
	$ua->ssl_opts( 'verify_hostname' => 0 );
	$ua->credentials(
		$host . ':' . $PORT,
		$REALM,
		$user => $pass
	);
	return $ua;
}

=head2 payload()

Constructs the HTTP POST payload for launching jobs. Returns an array reference of

script/cipresrun  view on Meta::CPAN


=item * B<Register your application>

Once you are registered as a REST API user and you are logged in, you can fill out the
following form:

L<https://www.phylo.org/restusers/createApplication!input.action>

=item * B<Creating your config.yml>

The credentials for the user, the application, and the server you will be talking to, need
to be entered in a YAML file with the following fields:

 ---
 URL: https://cipresrest.sdsc.edu/cipresrest/v1
 KEY: <your application key>
 CRA_USER: <your user name>
 PASSWORD: <your password>

=back



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