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Quick Start Guide | ||
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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. | ||
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It is based on `Nowakowski et al. 2017. <https://science.sciencemag.org/content/358/6368/1318.long>`_ | ||
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. | ||
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Step 1: Download the example dataset | ||
^^^^ | ||
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Download the data using curl:: | ||
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curl -ks https://cells.ucsc.edu/downloads/samples/mini.tgz | ||
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This file contains all the pieces necessary to create a simple cell browser. | ||
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Step 2: Unpack the dataset | ||
^^^^ | ||
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Next, we need to take this file and unpack it's contents:: | ||
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tar xvz mini.tgz | ||
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This will create a new ``mini`` directory contain the cell browser files. | ||
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Step 3: Enter the `mini` directory | ||
^^^^ | ||
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Now, enter the ``mini`` directory so that we can build the cell browser next:: | ||
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cd mini | ||
Step 4: Build the cell browser | ||
^^^^ | ||
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Then, build the cell browser:: | ||
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cbBuild -o ~/public_html/cells/ -p 8888 | ||
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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. | ||
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Step 5: Check it out! | ||
^^^^ | ||
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Finally, point your web browser to http://localhost:8888 to view your minimal cell browser. | ||
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Step 6: Stop webserver | ||
^^^^ | ||
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When you are done playing with your minimal cell browser, stop the web server started by cbBuild using ``Ctrl-C``. | ||
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.. | ||
Commenting this out for now | ||
---- | ||
Building your own Cell Browser | ||
^^^^ | ||
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The next page, "Setup Your Own", will describe the process of building a cell browser for your own dataset. |