Advanced Topics

Cell browser updates and web server configuration

New features and bug fixes are being added to the UCSC Cell Browser software all the time. You can update the javascript files and re-create the index.html using the command line tool cbUpgrade. You need to use the --code option and the -o to specify the output directory, e.g. cbUpgrade --code -o /var/www/cellbrowser/.

Your web server should support byte-range requests. This isn’t important for smaller, but for datasets with files larger than 30MB, a warning message will be shown once. Most web servers and web hosters support them by default. For Apache, byte-range requests are enabled by default but may need to be activated in some installations of nginx.

Default output directory for building cell browsers

The html directory can be defined in all tools with the option -o. If that becomes cumbersome, you can also permanently set it through the environment variable CBOUT (e.g. in your ~/.bashrc) or by adding a line like this to ~/.cellbrowser.conf:

htmlDir = "/data/www/cb/"

Google Analytics

To add Google Analytics tracking to your cell browser, create a file .cellbrowser.conf in your home directory and add a line like this:

gaTag = "UA-11231232-1"

Then run cbBuild or cbUpgrade to rebuild your index.html, after which it should contain your Google Analytics tracking code.

Various cellbrowser.conf configurations

For a reference of all possible cellbrowser.conf statements, see the example conf

If you have meta fields with very long names, you can reduce the font size. Configure them like this:

metaOpt = {‘Cluster_field’ : {‘fontSize’: ‘10px’}}

In your meta.tsv, you can have URLs to images. These will be shown on mouse over in the left annotation bar.

If you set the default coloring field to ‘None’ (without the quotes), then there is no coloring at all when the cell browser starts.

To change the coloring/label field automatically when the user activates some coordinates (layout), use the option “colorOnMeta” to specify the field:

    {"file":"tsne.coords.tsv", "shortLabel":"t-SNE on WGCNA"},
    # you can force coloring of some other meta data field when a layout is changed to another one
    {"file":"subset.coords.tsv", "shortLabel":"neural cells", colorOnMeta="neuralCluster"},

In very rare cases, it can be necessary to tell cbBuild that the numbers in the matrix are floating point numbers. The setting looks like this:

matrixType = "float"