Name: basespace-python-sdk
Owner: Basespace
Description: BaseSpace Python SDK
Created: 2012-08-16 17:17:41.0
Updated: 2017-12-22 00:41:19.0
Pushed: 2017-05-08 10:22:35.0
Homepage: null
Size: 2111
Language: Python
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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.
Morten Kallberg Eric Smith Peter Saffrey Mauricio Varea
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'.
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
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')
Update to support changes in BaseSpace REST specification version v1pre3. Specific changes are:
Initial release of BaseSpacePy
See License.txt in the basespace-python-sdk directory for details on licensing and distribution.