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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