Ensembl REST API

The Ensembl REST API provides language-agnostic, RESTful access to Ensembl data over HTTP. You can interact with the API by sending requests to the central REST server endpoint. This allows developers to programmatically retrieve genomic data using any programming language capable of making HTTP requests.

http://rest.ensembl.org

To use Highlight.js on a web page, include the library and a CSS theme, then call hljs.initHighlightingOnLoad(). The library will automatically find and highlight code blocks within <pre><code> tags, attempting to auto-detect the language.

If auto-detection fails, you can explicitly specify the language using the class attribute with the language- or lang- prefix (e.g., class="language-html").

To prevent a specific block from being highlighted, use the no-highlight class.

<link rel="stylesheet" href="/path/to/styles/default.css">
<script src="/path/to/highlight.pack.js"></script>
<script>hljs.initHighlightingOnLoad();</script>

<!-- Explicit language specification -->
<pre><code class="html">...</code></pre>

<!-- Disable highlighting for a block -->
<pre><code class="no-highlight">...</code></pre>

Highlight.js can be obtained in several ways:

• Hosted or custom-build browser script: Available via the official download page.
• Server module: For use in Node.js or other server-side environments.

Note: The library cannot be used directly from the GitHub source; it must be built first. If the pre-packaged options do not meet your needs, you will need to follow the building documentation.

For more control over what and when to highlight, use hljs.highlightBlock(block) and hljs.configure(options). This allows you to target specific elements instead of relying on the automatic <pre><code> pattern.

If you are using containers that do not preserve newlines (like <div>), you should configure Highlight.js to use <br> tags for line breaks using hljs.configure({useBR: true}).

// Example: Manual initialization using jQuery
$(document).ready(function() {
  $('pre code').each(function(i, block) {
    hljs.highlightBlock(block);
  });
});

// Example: Manual initialization with custom container and BR support
hljs.configure({useBR: true});

$('div.code').each(function(i, block) {
  hljs.highlightBlock(block);
});

Highlight.js can be integrated in several ways:

• CDN: Use a hosted version directly in the browser.
• Download: Download a custom build from the official download page.
• Server-side: Install it as a module for use in Node.js or other server environments.

Note: The library is not intended to be used directly from the GitHub source code; it requires a specific build. If the provided builds do not meet your needs, you can follow the build documentation.

For more control over when and what to highlight, use hljs.highlightBlock(block) and hljs.configure(options). This is useful if you are not using <pre><code> tags or if you need to trigger highlighting after specific events (like a DOM ready event).

If your code containers do not preserve line breaks, you must configure the library to use <br> tags by setting useBR: true in the configure method.

// Example: Manual highlighting using jQuery
$(document).ready(function() {
  $('pre code').each(function(i, block) {
    hljs.highlightBlock(block);
  });
});

// Example: Custom configuration and non-standard containers
hljs.configure({useBR: true});

$('div.code').each(function(i, block) {
  hljs.highlightBlock(block);
});

Use this Selenium test suite in the following scenarios:

• New EC2 Instances: When loading a new instance on Amazon EC2.
• Cache Population: When prodding the cache to ensure all examples are populated.

The tests in this directory are designed in SeleniumIDE and tested in Firefox 19. To execute the full suite, follow these steps:

1. Load the test suite: Open the TestSuite file in SeleniumIDE.
2. Configure the environment: Edit the environment test case within the suite to set the CurrentEnvironment variable to your specific server installation URL.
3. Execute: Run the test suite from within SeleniumIDE.

1). Load the test suite file *TestSuite*
2). Edit the environment test case to set the CurrentEnvironment to your server installation
3). Run the test suite

To run the Selenium tests in this repository, you must install the SeleniumIDE extension. SeleniumIDE installs directly into the Firefox browser.

Download it from: http://docs.seleniumhq.org/download/

The following options are available for the mysql_lookup.pl CLI tool:

--id=s        Specify a single stable ID to look up.
--file=s      Specify a file containing a list of stable IDs (one per line).
--type=s      Filter lookups by object type (e.g., gene, transcript).
--repeats=i   Number of times to repeat the lookup (default: 1).
--help        Display usage information.