Package: python_cipres
The CIPRES REST API (CRA) provides a way to run parallel versions of phylogenetic alignment and tree
inference software, such as RaXML, MrBayes, Garli, Beast, etc. on high performance supercomputers.
The python_cipres package is a client library that makes it easy to use the CRA.  The package includes
several scripts that can be run, as is, to submit jobs, check their status and download results.  Or,
the package can imported and used to develop custom software that uses the CRA.python_cipres has been tested on python 2.6, python 2.7 and python 3.4.3 on linux, mac OS and windows.InstallationTo install python_cipres, simply:$ pip install python_cipresOr, if you’ve downloaded the source from svn, or from a source archive, go to the top
level directory, which contains “setup.py”, and run:$ python setup.py installRegister to use the CIPRES REST APIRegister athttps://www.phylo.org/restusers, then log in, and from the “Developer” menu,
choose “Application Management” and create a new application.  Make note of the application ID that
is assigned.General documentation about using the CIPRES REST API is available athttps://www.phylo.org/restusers/documentation.  However, the documentation doesn’t specifically
address the python_cipres package.Configuration File (~/pycipres.conf)In your home directory create a file named “pycipres.conf” with the following settings:URL=https://cipresrest.sdsc.edu/cipresrest/v1
APPNAME=the_application_you_just_registered
APPID=application_ID
USERNAME=the_username_you_just_registered
PASSWORD=the_password
VERBOSE=TestRun a quick test of the installation and configuration:$ cipresjob.py -lThis should return the url of the CRA and a list of jobs that you’ve submitted.  Without any
submitted jobs it looks like this:URL=https://cipresrest.sdsc.edu/cipresrest/v1DocumentationThere are two scripts, tooltest.py and cipresjob.py that can be run from the command line to submit jobs
and monitor them.   The scripts are explained in examples/Readme.txt.You will find the examples directory where you installed the python_cipres package (the path
will typically be similar to site-packages/python_cipres-XX-py2.7.egg/python_cipres/examples) OR you can
download a source archive from the pypi page.  Within the expanded source archive, the path is
python_cipres/examples.   Each subdirectory under examples is a “job template” that can be
submitted to the CRA using tooltest.py.To use the python_cipres library in your own code:import python_cipres.client as CipresClientThe API provided by the python_cipres library is not documented yet, however it is quite small and
simple.  It is implemented entirely in client.py.  Commands.py uses the API to implement the
functionality provided by tooltest.py and cipresjob.py, so looking at commands.py is a good way
to see how to use the API.client.pyprovides the basic job management APIcommands.pyuses the methods in client.py to implement what tooltest.py and cipresjob.py dobin/tooltest.py and bin/cipresjob.pyare executable scripts that call the corresponding methods in commands.py.
Tooltest.py submits a job to CIPRES based on the specification in a job template directory.
Cipresjob.py lists jobs, checks a job’s status and downloads results.Please subscribe to the cipres-rest-users mailing list athttps://groups.google.com/forum/#!forum/cipres-rest-users.
Send a message to the list if you have any questions about how to use the API or how to configure a specific tool.Distributing your codeIf you create scripts or an application that uses the CIPRES REST API and you share your code with others,
keep in mind that the users of your code should use the same APPNAME and APPID that you registered,
to identify your code, but must use their own USERNAME and PASSWORD to submit jobs.Web ApplicationsIf you are submitting jobs from a web application that has multiple users, then as a matter of policy,
you must register your application as an umbrella application, as explained in the “Register” section
of the User Guide (https://www.phylo.org/restusers/docs/guide.html).  Web applications can’t use
tooltest.py and cipresjob.py, as is, because they don’t support umbrella authentication; however
you can use the code that implements tooltest.py and cipresjob.py (see commands.py) as a template for
your own code. The only change you would need to make is that you must pass an additional dictionary
argument, endUserHeaders, to the CipresClient.Client() ctor, as shown in a comment in commands.py.
The endUserHeaders identifies the end user, of your application, for whom the cipres request
is being made.Release History0.9 (2016-03-24)Parse and return metadata if present in job status0.8 (2015-06-15)Modified to work with python 3 as well as python 2.0.7 (2015-06-05)client.py can be used with DIRECT or UMBRELLA authentication now.  If using umbrella
authentication, add the endUserHeaders dictionary when instantiating CipresClient.Client.Accepts job submission parameters with or without the “input.”, “vparam.”, and “metadata.”
prefixes that are documented inhttps://www.phylo.org/restusers/docs/guide.html#SubmitJobsandhttps://www.phylo.org/restusers/docs/tools.  For example, both “runtime_=0.25” and
“vparam.runtime_=0.25” work with python_cipres.The tool to run may be specified with either “tool” or “toolId”.VERBOSE property is no longer required in ~/pycipres.conf.0.5 (2015-06-02)Added -r argument to cipresjob.py to cancel and remove jobs.0.4 (2015-06-01)Initial version on pypi