INTRODUCTION

BaseSpacePy is a Python based SDK to be used in the development of Apps and scripts for working with Illumina's BaseSpace cloud-computing solution for next-gen sequencing data analysis.

The primary purpose of the SDK is to provide an easy-to-use Python environment enabling developers to authenticate a user, retrieve data, and upload data/results from their own analysis to BaseSpace.

If you haven't already done so, you may wish to familiarize yourself with the general BaseSpace developers documentation (https://developer.basespace.illumina.com/) and create a new BaseSpace App to be used when working through the examples provided in 'examples' folder.

AUTHORS

Morten Kallberg Eric Smith

REQUIREMENTS

Python 2.6 with the packages 'pycurl', and 'python-dateutil' installed. You can install these on Ubuntu with 'apt-get install python-pycurl' and 'apt-get install python-dateutil'.

The multi-part file upload will currently only run on a unix setup.

INSTALL

Version 0.1.2 of BaseSpacePy can be checked out here:

git clone https://github.com/basespace/basespace-python-sdk.git

To install 'BaseSpacePy' run the 'setup.py' script in the main directory (for a global install you will need to run this command with root privileges):

cd basespace-python-sdk/src
python setup.py install

If you do not have root access, you may use the --prefix to specify the install dir (make sure this dir is in your PYTHONPATH):

python setup.py install --prefix=/folder/in/my/pythonpath

For more install options type:

python setup.py --help

Alternatively you may include the src directory in your PYTHONPATH by:

export PYTHONPATH=$PYTHONPATH:/my/path/basespace-python-sdk/src

or add it to the PYTHONPATH at the top of your Python scripts using BaseSpacePy:

import sys
sys.path.append('/my/path/basespace-python-sdk/src')
import BaseSpacePy

To test that everything is working as expected, launch a Python prompt and try importing 'BaseSpacePy':

mkallberg@ubuntu:~/$ python
>>> import BaseSpacePy

CHANGELOG

v 0.1.2

• Added use of os.path.join when forming path in file-download from a Sample
• Added support for custom http-timeouts in the BaseSpaceAPI class
• Added link to Sample class in AppResult class
• Introduced method getAppSessionByID in BaseSpaceAPI
• Introduced the new fields IsPairedEnd, Read1, Read2, NumReadsRaw, and NumReadsPF to the Sample class
• Introduced new date format

v 0.1.1

Update to support changes in BaseSpace REST specification version v1pre3. Specific changes are:

• AppLaunchResponse is now AppSessionResponse
• AppLaunch is now AppSession and has been updated to include the fields additional fields
• Analysis is now AppResult
• An Application object has been added to the data model as part of the new AppSession
• AppResults (previously Analysis) do no longer have a setStatus method, this logic has been moved to the AppSession class

v 0.1

Initial release of BaseSpacePy

COPYING / LICENSE

See License.txt in the basespace-python-sdk directory for details on licensing and distribution.

KNOWN BUGS