Native Installation

Steps to Native Installation

1. Install GLUE Software Framework
   If you haven't installed GLUE yet, follow the native installation instructions in the GLUE User Guide.

2. Download the Lentivirus-GLUE Repository
   Clone or download the Lentivirus-GLUE repository from its official location.

3. Download & Load the Prebuilt Database

   Prebuilt versions of the Lentivirus-GLUE database are available for different extensions. Select and download the appropriate version for your needs:

   • Lentivirus-GLUE core project:
     Download lentivirus_glue.sql.gz

   • Lentivirus-GLUE core project + SRLV extension:
     Download lentivirus_glue_srlv.sql.gz

   • Lentivirus-GLUE core project + FIV extension:
     Download lentivirus_glue_fiv.sql.gz

   • Lentivirus-GLUE core project + EIAV extension:
     Download lentivirus_glue_eiav.sql.gz

   • Lentivirus-GLUE core project + Bovine extension:
     Download lentivirus_glue_bovine.sql.gz

   • Lentivirus-GLUE core project + ERV extension:
     Download lentivirus_glue_erv.sql.gz

   Once you've downloaded the desired .sql.gz file, decompress it and load it into your local MySQL system. Adjust the commands below to match your MySQL installation:

gunzip lentivirus_glue.sql.gz

/usr/local/mysql/bin/mysql --user=gluetools --password=glue12345 GLUE_TOOLS < lentivirus_glue.sql

4. Verify Installation
   Start the GLUE command-line interpreter and verify that the project has been loaded:

Mode path: /
GLUE> list project
+==============+==============================================================+
|     name     |                        description                           |
+==============+==============================================================+
| lentivirus   | A GLUE project for lentivirus comparative genomics           |
+==============+==============================================================+
Projects found: 1
Mode path: /
GLUE>

Local Project Build

Alternatively, if you prefer to build the project locally from scratch, follow these steps:

1. Navigate to the Lentivirus-GLUE Directory

2. Start the GLUE Command-Line Interpreter

3. Build the Core Project

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

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> run file buildCoreProject.glue

This will build the base or 'core' project, which contains a minimal set of feature definitions, clade categories, reference sequences, and alignments.

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