NAME

cipresrun - command line interface to the CIPRES analysis portal

SYNOPSIS

 cipresrun \
     -t <tool> \
     -p <paramname=paramvalue> [-p <paramname=paramvalue>] \     
     -i <infile> \
     -y <config.yml> \
     -o <out.name=/out/path> [-o <out.name=/out/path>] \
     -w <workdirectory> \
     [-v] [-h] [--manpage]

OPTIONS AND ARGUMENTS

-v or --verbose

Increases the verbosity of the process. This is useful to see what is being returned by the server, for example to figure out what your tool is producing as output files. A good approach is to first do a small run (e.g. a small data file) under verbose, see what's going on, and then improve your parameter settings for bigger analyses under lower verbosity.

-h or --help

Prints usage message and quits.

-m or --manpage

Prints larger manual page and quits.

-t toolname or --tool=toolname

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

https://www.phylo.org/restusers/docs/tools

For example: MAFFT_XSEDE

-p key=value or --param key=value

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

-i filename or --infile=filename

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

-o key=value or --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 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 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 STDERR, 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 -v (verbose) flag and then consulting the XML that is produced by the final step. I.e. this is not well documented by CIPRES.

-w dirname or --workdir=dirname

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

-y config.yml or --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:

• Register yourself

  This is done by filling out the following web form:

  https://www.phylo.org/restusers/register.action

• Register your application

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

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

• 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>

SEE ALSO

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