Quick Start Guide

These steps will walk through downloading and setting a minimal cell browser using an example dataset. It is assumed that you are carrying out these steps locally on your computer.

It is based on Nowakowski et al. 2017. and the corresponding https://cortex-dev.cells.ucsc.edu dataset. The expression matrix only includes 100 genes, but it does show off many of the features of the cell browser.

Step 1: Download the example dataset

Download the data using curl:

curl -ks https://cells.ucsc.edu/downloads/samples/mini.tgz

This file contains all the pieces necessary to create a simple cell browser.

Step 2: Unpack the dataset

Next, we need to take this file and unpack it’s contents:

tar xvz mini.tgz

This will create a new mini directory contain the cell browser files.

Step 3: Enter the mini directory

Now, enter the mini directory so that we can build the cell browser next:

cd mini

Step 4: Build the cell browser

Then, build the cell browser:

cbBuild -o ~/public_html/cells/ -p 8888

The -o option specifies the output directory and -p defines the port to used for the webserver. A bunch of information will be displayed on the screen, mostly just reporting its progress in building the cell browser.

Step 5: Check it out!

Finally, point your web browser to http://localhost:8888 to view your minimal cell browser.

Step 6: Stop webserver

When you are done playing with your minimal cell browser, stop the web server started by cbBuild using Ctrl-C.