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Loading Local Data

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You may also want to see the Chromoscope Python package, which allows you to load local files on computational notebooks.

You can run a local file server to display local files on Chromoscope. This enables you to safely visualize your private files. There are multiple light and easy-to-install file servers. In this page, we will use http-server for the demonstration.

Run Local File Server​

You first need to install the file server called http-server. To install it, you need to first install a package manager, npm.

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To install npm, please refer to the official documentation: https://docs.npmjs.com/downloading-and-installing-node-js-and-npm#using-a-node-installer-to-install-node-js-and-npm

After installing the npm, you can use it to install http-server. For example, run the following command on your terminal.

npm install http-server -g

Now you can run the server on the designated folder.

http-server ./path-to-your-folder --cors -c-1

Note that the --cors option allows the browser to access your files.

Now, you can browse files that are located under the selected folder using your browser. For example, open http://127.0.0.1:8080/ on the browser.

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Also see https://stackoverflow.com/a/16350826

Create Data Config​

Using the URL of the local files, you can make a data config. For example, the following example specify two local files (i.e., SV and CNV).

{
    "id": "SRR7890905",
    "cancer": "breast",
    "assembly": "hg38",
    "sv":  "http://127.0.0.1:8080/SVTYPE_SV_test_tumor_normal_with_panel.bedpe",
    "cnv": "http://127.0.0.1:8080/SRR7890943.ascat.v3.cnv.tsv"
}
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You can download the following files to test this.

Use Local Data Config​

You can also put this local data config (say, local-config.json) under the folder hosted by your http-server. You should be able to open the data config file on the browser using http://127.0.0.1:8080/local-config.json.

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If you open the following URL, you should be able to open the data config on your browser.

http://127.0.0.1:8080/local-config.json

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Open Browser​

As a last step, use the data config you created to browse your local files in Chromoscope.

https://chromoscope.bio/app/?external=http://127.0.0.1:8080/local-config.json

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