Some notes on the setup of GenePattern Notebook environment.
IMPORTANT: The current version of the code only works with GenePattern 3.9.3 and up! Some features are only supported in GenePattern 3.9.5 and up.
In order to get the GenePattern Notebook working you will first need to install a compatible version of Python. This means you will need either Python 2.7 or Python 3.4+.
Note for Mac Users: Mac comes with Python, but - depending on the version OSX you have - you may have to update to a new version. To do this I would recommend using a package manager such as Homebrew or MacPorts.
You may wish to install the Anaconda distribution of Python from Continuum Analytics. This is a scientific version of Python that ships with many of the most popular Python packages for science, math and data analysis (ex: NumPy, SciPy, Pandas, Matplotlib, IPython, etc.).
Install PIP (Python Package Index) if not already installed (PIP may come with Anaconda distribution; see https://pip.pypa.io/en/latest/installing.html). This is Python's preferred package management system.
The best way to install GenePattern Notebook is through PIP. It can be installed by executing the following command:
pip install genepattern-notebook
Finally, you may launch Jupyter Notebook by issuing the following command at the terminal:
jupyter notebook
This will start up the notebook kernel and launch your web browser pointing to the Notebook.
If you want to update GenePattern Notebook to a more recent version on PIP, run the following command:
pip install -U --no-deps genepattern-notebook
Users using the GenePattern Notebook with an older version of GenePattern (3.9.3 or 3.9.4) may need to log into the GenePattern UI before making use of the notebook. The server status message and child jobs will also be unavailable.
Most common GenePattern features are supported in the GenePattern Notebook. A few, however, have yet to be implemented. GenePattern features that are not yet supported are:
- Batch job submission
- GenomeSpace integration
- Dynamically updated choice parameters
- Parameter groups