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## Installation

If you have not done so already, install the GLUE software framework by following the [installation instructions](http://glue-tools.cvr.gla.ac.uk/#/installation) on the GLUE web site:

Note the HCV-GLUE project has a layered structure. This approach simplifies project management because it allows data items that are likely to be used across a wide range of analysis contexts to be maintained separately from those only required for more specialized purposes. The ‘base’ layer of HCV-GLUE contains only a minimal set of essential data items required for comparative analysis.

To build the base (or 'core') project, download the HCV-GLUE repository, navigate into the top-level directory, and start the GLUE command line interpreter, e.g.:

```
rob$ gluetools.sh
GLUE Version 1.1.107
Copyright (C) 2015-2020 The University of Glasgow
This program comes with ABSOLUTELY NO WARRANTY. This is free software, and you
are welcome to redistribute it under certain conditions. For details see
GNU Affero General Public License v3: http://www.gnu.org/licenses/
Mode path: /
GLUE>
```

At the GLUE command prompt, run the 'buildCoreProject.glue' file as follows:

`GLUE> run file hcvProject.glue`

This will build the base project, which contains a minimal set of HCV 'reference' sequences. The base project can be extended to incorporate all HCV sequences in GenBank by downloading the extension project [NCBI-HCV-GLUE](https://github.com/giffordlabcvr/NCBI-HCV-GLUE).
Please visit **[the HCV GLUE web page](http://hcv-glue.cvr.gla.ac.uk/#/aboutGlueProject)** for instructions on installing HCV-GLUE.

## Usage

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