NAME

Bio::CIPRES - interface to the CIPRES REST API

SYNOPSIS

    use Bio::CIPRES;

    my $ua = Bio::CIPRES->new(
        user    => $username,
        pass    => $password,
        app_id  => $id,
        timeout => 60,
    );

    my $job = $ua->submit_job( %job_params );

    while (! $job->is_finished) {
        sleep $job->poll_interval;
        $job->refresh_status;
    }

    if ($job->exit_code == 0) {

        print STDOUT $job->stdout;
        print STDERR $job->stderr;
        for my $file ($job->list_outputs) {
            $file->download( $file->name );
        }

    }
    

DESCRIPTION

Bio::CIPRES is an interface to the CIPRES REST API for running phylogenetic analyses. Currently it provides general classes and methods for job submission and handling - determination of the correct parameters to submit is up to the user (check "SEE ALSO" for links to tool documentation).

METHODS

new

    my $ua = Bio::CIPRES->new(
        user    => $username,
        pass    => $password,
        app_id  => $id,
        timeout => 60,
    );

    # or read configuration from file

    my $ua = Bio::CIPRES->new(
        conf => "$ENV{HOME}/.cipres"
    );

Create a new Bio::CIPRES object. There are three required parameters: username (user), passphrase (pass), and application ID (app_id). These can either be passed in on the constructor or read in from a configuration file, as demonstrated above. The configuration file should contain key=value pairs, one pair per line, as in:

    user=foo
    pass=bar
    app_id=foo_bar_baz

The passphrase must be stored in plaintext, so the usual precautions apply (e.g. the file should not be world-readable). If possible, find another way to retrieve the passphrase within your code and pass it in directly as a method argument.

submit_job

    my $job = $ua->submit_job( %params );

Submit a new job to the CIPRES service. Params are set based on the tool documentation (not covered here). Returns a Bio::CIPRES::Job object.

list_jobs

    for my $job ( $ua->list_jobs ) {
        # do something
    }

Returns an array of Bio::CIPRES::Job objects representing jobs in the user's workspace.

get_job_by_handle

    my $job = $ua->get_job_by_handle( $job_handle );

Takes a single argument (string containing the job handle/ID) and returns a Bio::CIPRES::Job object representing the appropriate job, or undef if not found.

CAVEATS AND BUGS

Please report bugs to the author.

AUTHOR

Jeremy Volkening <jdv@base2bio.com>

COPYRIGHT AND LICENSE

Copyright 2016 Jeremy Volkening

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.