isb-cgc / examples-python

Analysis examples based on the ISB-CGC hosted TCGA data, using Python and IPython Notebooks.

examples-Python

This repository contains a series of Python examples to get you started using the data and tools provided by the ISB-CGC on the Google Cloud Platform.

• notebooks: this directory contains tutorials in the form of IPython notebooks;
• python: this directory contain tutorials in the form of simple python scripts.

Important Note

If you launch your own Cloud Datalab instance, please be sure to shut it down when you are no longer using it. A typical Google Cloud Datalab VM will cost your project approximately $1/day. Shut down instructions and other tips are here -- look for the section called Stopping/Starting VM Instances.

Requirements

• google-api-python-client
• oauth2client
• httplib2
• requests

examples-python's Issues

google-api-python-client is in maintenance only mode

The old Google client libraries (google-api-python-client) are now in maintenance only mode. They are superseded by google-cloud-python.

Most of the notebooks need to be updated to be kept up-to-date.

Schema not rendered in iPython notebook

On https://github.com/isb-cgc/examples-Python/blob/master/notebooks/Creating%20TCGA%20cohorts%20--%20part%201.ipynb, there is a call to

%bigquery schema --table isb-cgc:tcga_201607_beta.Clinical_data

which displays no schema details underneath. This is an issue with the rendering code relying on JavaScript and github blocking JavaScript.

I just filed an issue there ("%bigquery schema --table" produces no visible output on github)[https://github.com/googledatalab/pydatalab/issues/184] which includes some python code to replace "bigquery schema" call. This can be used to work around the pydatalab library issue.