python_cipres 0.4

Installation

To install python_cipres, simply:

$ pip install python_cipres

Or, 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 install

Register to use the CIPRES REST API

Register at https://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 at https://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=

Test

Run a quick test of the installation and configuration:

$ cipresjob.py -l

This 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/v1

Documentation

There 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 site-packages/python_cipres-0.1-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 run on the CRA using tooltest.py.

To use the python_cipres library in your own code:

import python_cipres.client as CipresClient

Have a look at the code in commands.py to see how to use client.py.

client.py

provides the basic job management API

commands.py

uses the methods in client.py to implement what tooltest.py and cipresjob.py do

bin/tooltest.py and bin/cipresjob.py

are 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.

If you base an application on python_cipres and share it with others, keep in mind that the users of your application should use the APPNAME and APPID that you registered to identify your code, but must use their own USERNAME and PASSWORD to submit jobs.