### Configure Ensembl REST API Setup

Source: https://github.com/ensembl/ensembl-rest/wiki/REST-Installation-and-Development

Run Makefile.PL after installing dependencies to confirm the setup.

```bash
perl Makefile.PL
```

--------------------------------

### Catalyst Server Startup Output

Source: https://github.com/ensembl/ensembl-rest/wiki/REST-Installation-and-Development

Example output when the Catalyst server starts, indicating the version and the address where it is accepting connections.

```text
2012/09/05 11:01:54 (0) Catalyst.pm 1184> EnsEMBL::REST powered by Catalyst 5.90015 
HTTP::Server::PSGI: Accepting connections at http://0:3000/
```

--------------------------------

### Install Faidx XS Library

Source: https://github.com/ensembl/ensembl-rest/wiki/REST-Installation-and-Development

Clone the faidx_xs repository and install the library using its Makefile.

```bash
git clone --branch master --depth 1 https://github.com/Ensembl/faidx_xs.git
(cd faidx_xs && perl Makefile.PL && make && make install)
```

--------------------------------

### Install Ensembl REST API from Git

Source: https://github.com/ensembl/ensembl-rest/wiki/REST-Installation-and-Development

Clone the ensembl-rest repository from GitHub to get the latest stable release.

```bash
git clone https://github.com/Ensembl/ensembl-rest.git
```

--------------------------------

### Install Tabix Library

Source: https://github.com/ensembl/ensembl-rest/wiki/REST-Installation-and-Development

Download, compile, and install the Tabix library and its Perl bindings.

```bash
wget https://github.com/samtools/tabix/archive/master.tar.gz
tar zxf master.tar.gz
(cd tabix-master && make)
(cd tabix-master/perl && perl Makefile.PL && make)
```

--------------------------------

### Python Request Example

Source: https://github.com/ensembl/ensembl-rest/wiki/Scripting:-Request-Variables

This snippet shows how to make a GET request using the requests library in Python. It defines server and extension strings and prints the response.

```python
import requests, sys
server = "https://rest.ensembl.org"
ext = "/lookup/id/ENSG00000157764?expand=1"
r = requests.get(server+ext, headers={ "Accept" : "application/json"})
pprint (r)
```

--------------------------------

### R Request Example

Source: https://github.com/ensembl/ensembl-rest/wiki/Scripting:-Request-Variables

This snippet demonstrates making a GET request in R using the httr and jsonlite libraries. It constructs the URL from server and extension strings and displays the response.

```r
library(httr)
library(jsonlite)
server <- "https://rest.ensembl.org"
ext <- "/lookup/id/ENSG00000157764?expand=1"
r <- GET(paste(server, ext, sep = ""), accept("application/json"))
r
```

--------------------------------

### Install Catalyst Runtime and Devel with CPANMINUS

Source: https://github.com/ensembl/ensembl-rest/wiki/REST-Installation-and-Development

Use cpanm to install Catalyst dependencies if using local::lib.

```bash
cpanm Catalyst::Runtime Catalyst::Devel
```

--------------------------------

### Install Ensembl REST API Dependencies with cpanm

Source: https://github.com/ensembl/ensembl-rest/wiki/REST-Installation-and-Development

Navigate to the ensembl-rest directory and install local dependencies using cpanm.

```bash
cd ensembl-rest
cpanm --installdeps .
```

--------------------------------

### VEP Plugin Configuration Example

Source: https://github.com/ensembl/ensembl-rest/blob/release/116/t/test-genome-DBs/testdata/vep_plugin_config.txt

Defines the configuration for a VEP plugin, including its key, parameters, availability, and enabled status. This example shows the RestTestPlugin configuration.

```perl
my $VEP_PLUGIN_CONFIG = {
  "plugins" => [

    # test
    {
      "key" => "RestTestPlugin",
      "params" => [ '@*' ],
      "available" => 1,
      "enabled" => 0,
    },
  ]
};

```

--------------------------------

### GET Request - Accept Header

Source: https://github.com/ensembl/ensembl-rest/wiki/Output-formats

Shows how to specify the desired output format for a GET request using the 'Accept' HTTP header, which is the generally recommended method.

```APIDOC
## GET /info/ping

### Description
Requests information about the API's status, allowing specification of the output format via the 'Accept' HTTP header.

### Method
GET

### Endpoint
http://rest.ensembl.org/info/ping

### Parameters
#### Headers
- **Accept** (string) - Required - Specifies the desired output format, e.g., `application/json`.

### Request Example
```bash
curl -H "Accept: application/json" \
http://rest.ensembl.org/info/ping
```
```

--------------------------------

### Build and Run the Client

Source: https://github.com/ensembl/ensembl-rest/wiki/Example-Java-Client-with-Unirest

After placing the client code in the correct directory, use Maven to build an executable JAR and then run it from the command line.

```bash
mvn clean compile assembly:single
java -jar target/EnsemblRestClient-1.0-SNAPSHOT-jar-with-dependencies.jar
```

--------------------------------

### GET Request with Optional Parameter and Content-Type

Source: https://github.com/ensembl/ensembl-rest/wiki/Getting-Started

Example of a GET request to the lookup/id endpoint, specifying the content type as JSON. This ensures the response is formatted in JSON.

```bash
$ curl 'https://rest.ensembl.org/lookup/id/ENSG00000165029?expand=1' -H 'Content-type:application/json'
```

--------------------------------

### GET Request with Optional Parameter

Source: https://github.com/ensembl/ensembl-rest/wiki/Getting-Started

Example of a GET request to the lookup/id endpoint with an optional 'expand' parameter. Use this to retrieve detailed information about a gene, including its transcripts, translations, and exons.

```bash
$ curl 'https://rest.ensembl.org/lookup/id/ENSG00000165029?expand=1'
```

--------------------------------

### Compile and Run Java Client

Source: https://github.com/ensembl/ensembl-rest/wiki/Example-Java-Client

Instructions for compiling the Java client with its dependency and running the application. Ensure the json-smart JAR is available.

```bash
javac -cp json-smart-1.2.jar RestClient.java
java -cp .:json-smart1.2.jar RestClient
```

--------------------------------

### Basic Initialization with initHighlightingOnLoad

Source: https://github.com/ensembl/ensembl-rest/blob/release/116/root/static/js/highlight/README.md

Include the stylesheet and script, then call initHighlightingOnLoad to automatically highlight code within <pre><code> tags on page load.

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

--------------------------------

### Perl Request Example

Source: https://github.com/ensembl/ensembl-rest/wiki/Scripting:-Request-Variables

This snippet illustrates how to make a GET request in Perl using HTTP::Tiny and JSON. It defines server and extension variables and prints the request result.

```perl
use HTTP::Tiny;
use JSON;
my $http = HTTP::Tiny->new();
my $server = "https://rest.ensembl.org";
my $ext = "/lookup/id/ENSG00000157764?expand=1";
my $headers = { 'Accept' => 'application/json' };
my $r = $http->get($server.$ext, {headers => $headers});
print $r;
```

--------------------------------

### Configure Test Databases for Ensembl REST

Source: https://github.com/ensembl/ensembl-rest/wiki/REST-Installation-and-Development

Copy the example test database configuration file and edit it to set appropriate connection settings for running the test server.

```bash
cd ensembl-rest
cp t/MultiTestDB.conf.example t/MultiTestDB.conf
$EDITOR t/MultiTestDB.conf
```

--------------------------------

### GET Request - Content-Type Parameter

Source: https://github.com/ensembl/ensembl-rest/wiki/Output-formats

Illustrates specifying the output format for a GET request by appending it as a 'content-type' query parameter.

```APIDOC
## GET /info/ping

### Description
Requests information about the API's status, allowing specification of the output format via the 'content-type' query parameter.

### Method
GET

### Endpoint
http://rest.ensembl.org/info/ping

### Parameters
#### Query Parameters
- **content-type** (string) - Required - Specifies the desired output format, e.g., `application/json`.

### Request Example
```bash
curl http://rest.ensembl.org/info/ping?content-type=application/json
```
```

--------------------------------

### Download and Install Ensembl API from Tarball

Source: https://github.com/ensembl/ensembl-rest/wiki/REST-Installation-and-Development

Fetch the Ensembl API from the stable branch tarball and unpack it.

```bash
wget ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz
tar zxvf ensembl-api.tar.gz
```

--------------------------------

### Specify JSON Output via Content-Type Parameter (GET)

Source: https://github.com/ensembl/ensembl-rest/wiki/Output-formats

Use the 'content-type' URL parameter to request JSON output for a GET request.

```bash
curl http://rest.ensembl.org/info/ping?content-type=application/json
```

--------------------------------

### Custom Initialization with highlightBlock and jQuery

Source: https://github.com/ensembl/ensembl-rest/blob/release/116/root/static/js/highlight/README.md

Iterate over code blocks using jQuery and apply highlighting individually with hljs.highlightBlock for more control over initialization.

```javascript
$(document).ready(function() {
  $('pre code').each(function(i, block) {
    hljs.highlightBlock(block);
  });
})
```

--------------------------------

### Specify JSON Output via Content-Type Header (GET)

Source: https://github.com/ensembl/ensembl-rest/wiki/Output-formats

Use the 'Content-Type' HTTP header to request JSON output for a GET request.

```bash
curl -H "Content-Type: application/json" \
http://rest.ensembl.org/info/ping
```