# JBrowse

**Installation**

1. Download the jbrowse.zip file and unzip into plugins directory.
2. Edit database details in `services/settings.php` file.

**Manual installation from JBrowse.org - optional**

Following steps are important when you need to convert existing JBrowse into GenIE module.

1. Copy JBrowse into plugins folder
2. Copy `index.php` into jbrowse folder
3. Create menu item called jbrowse
4. Change plugins `plugins/jbrowse/main.css` and `plugins/jbrowse/genome.css`
5. Copy `pugins/jbrowse/index.html` into `plugins/jbrowse/tool.php` from jbrowse.zip
6. Copy `plugins/jbrowse/src/dojo/dojo.css` from jbrowse.zip
7. Copy `plugins/jbrowse/src/dijit/theme/tundra/tundra.css` from jbrowse.zip

**Loading data into JBrowse**

```
bin/prepare-refseqs.pl --fasta [genome fasta file]
bin/flatfile-to-json.pl --gff [GFF3 file]] --trackLabel [Label name] --trackType CanvasFeatures
bin/generate-names.pl -v
```

**Usage**

Navigate to `http://[your server name]/genie/jbrowse`

For more information please go to [JBrowse documentation](http://gmod.org/wiki/JBrowse_Configuration_Guide)


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# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://geniesys.gitbook.io/geniesys/for-administrators/jbrowse.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.