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

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
HPC infrastructure. The portal has a web browser (point and click) interface, but also
a web service interface that can be interacted with using RESTful commands. The basic
workflow is as follows:

=over

=item * B<Launch a job>
This is done by issuing an HTTP POST request that includes: 1) HTTP authentication (i.e.
a user name and password that is registered to the realm), 2) uploading input data, 3)
configuration options for the job. The result value is an XML document that reports the
status. If all goes well, this will report that the job was launched successfully, and it
gives a URL to visit to check up on the status.

=item * B<Check job status>
The job URL is visited periodically (at most once every 60 seconds, as per CIPRES policy).
This is done using an authenticated GET request where the return value is an XML document
that reports whether the job has finished. Once it is finished, the document will include
a link to another document that lists the output data, which will be named (e.g. 
C<output.mafft>) and which will be identifiable by a URL from whence the data can be