BaseSpace Python SDK
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README.md

README.md

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 Peter Saffrey Mauricio Varea

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'.

INSTALL

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

GETTING STARTED

For most API calls, you will need credentials from an app. To create an app, go to the BaseSpace developer portal and create one. Naviagate to the Credentials tab of your app in the developer portal.

You can 1) store your credentials in a config file or 2) provide them as arguments to methods. To use a config file, create a file in your home directory named '.basespacepy.cfg'. Make this file readable and writeable by only you ('chmod 600 ~/.basespacepy.cfg'). Then add the following content to the file, and add your app's credentials (appSessionId is not required for many methods):

[DEFAULT]
name = my new app
clientKey =
clientSecret =
accessToken =
appSessionId =
apiServer = https://api.basespace.illumina.com/
apiVersion = v1pre3

Now you can get started quickly with code such as:

from BaseSpacePy.api.BaseSpaceAPI import BaseSpaceAPI
myAPI = BaseSpaceAPI()
user = myAPI.getUserById('current')

CHANGELOG

v 0.2

  • Added support for large-file (multipart) upload and download.
  • Added methods to get a Run's Files or Samples
  • Added support for a config file to store credentials
  • Made consistent all queryParameter arguments to accept objects (not dicts)
  • Added unit tests for all methods (except Billing and some MultipartFileTransfer methods)

v 0.1.2

  • Added support for getting item Properties
  • Added support for purchases and refunds
  • 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