view release on metacpan or  search on metacpan

script/cipresrun  view on Meta::CPAN

Prints larger manual page and quits.

=item C<-t toolname> or C<--tool=toolname>

Name of the analysis tool to run, as listed here:

L<https://www.phylo.org/restusers/docs/tools>

For example: C<MAFFT_XSEDE>

=item C<-p key=value> or C<--param key=value>

A key/value pair that configures something about the tool. For example:
C<-p vparam.runtime_=7.5> to configure the maximum run time. Consult the 
B<REST Tool Info> page of the CIPRES documentation for the respective tools. This option
can be used multiple times.

=item C<-i filename> or C<--infile=filename>

Path to an input file to analyze, e.g. an unaligned FASTA file.

=item C<-o key=value> or C<--key=value>

This is the name of a specific output type that CIPRES generates followed by the location
where to write that output to file on the client side. In other words, this is B<not> a 
free form name for you to choose. It's one of the multiple outputs that the
analysis can produce. For example, the alignment produced by MAFFT is called 
C<output.mafft>. That is the name you need to specify here if you want that output 
returned, followed by where you want this to be written, e.g. /home/user/result.fasta. 
You can also fetch things such as C<STDERR>, C<STDOUT>, and so on. Which outputs
are produced by a specific tool can (to the best of my knowledge) only be figured out by
running this program with the C<-v> (verbose) flag and then consulting the XML that is
produced by the final step. I.e. this is not well documented by CIPRES.

=item C<-w dirname> or C<--workdir=dirname>

The name of a directory to which to write the output files.

=item C<-y config.yml> or C<--yaml=config.yml>

The CIPRES portal requires authentication (i.e., a user name and password), as well as an
application key for your application. These can be obtained by taking the following steps:

=over

=item * B<Register yourself>

This is done by filling out the following web form:

L<https://www.phylo.org/restusers/register.action>

=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

=back

=head1 SEE ALSO

This program is implemented by a package module whose documentation may be instructive as
well. This can be found at L<Bio::Phylo::CIPRES>.

=cut