InteLIS

Integrated Laboratory Information & Sample Tracking System Simple, open-source LIS to manage and track samples for HIV VL, EID, TB, Hepatitis, COVID-19, CD4 and other priority diseases.

InteLIS (formerly VLSM) digitizes laboratory workflows — from sample collection to result dispatch — for national and sub-national health programs.

It's lightweight, self-hostable, and works both online and offline.

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📁 Table of Contents

• InteLIS
  • 📁 Table of Contents
  • ⚖️ License
  • 📋 Pre-requisites
  • 🚀 Installation
    • Option 1 — Automated Installation (Ubuntu LTS only)
    • Option 2 — Manual Installation
      • Step 1 — Get the code
      • Step 2 — Install dependencies
      • Step 3 — Set up the database
      • Step 4 — Configure the application
      • Step 5 — Set up Apache virtual host
      • Step 6 — Set up the cron job
  • ✅ Complete the Setup
  • 🔄 Updating InteLIS
    • Option 1 — Automated Update (Ubuntu LTS only)
    • Option 2 — Manual Update
  • 💬 Support

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⚖️ License

InteLIS is released under the InteLIS Community Copyleft License (Non-Commercial), Version 1.0.

This license allows non-commercial use — including public or private laboratories, healthcare programs, NGOs, research, and education — but restricts commercial redistribution or resale of the software.

For commercial licensing inquiries, contact [email protected]

See the full license text in LICENSE.md.

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📋 Pre-requisites

• Apache 2.x (with rewrite and headers modules enabled)
• MySQL 5.7 or higher
• PHP 8.2.x
• Composer

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🚀 Installation

Option 1 — Automated Installation (Ubuntu LTS only)

Supports Ubuntu 22.04 and above (LTS versions only)

cd ~
sudo wget -O setup.sh https://github.com/deforay/intelis/raw/master/scripts/setup.sh
sudo chmod +x setup.sh
sudo ./setup.sh
sudo rm setup.sh
exit

When prompted, enter:

• MySQL password
• STS URL
• Hostname (optional, default is intelis)

After the script completes:

1. Edit the config file with your MySQL details:

   sudo gedit /var/www/intelis/configs/config.production.php

2. Continue with Complete the Setup.

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Option 2 — Manual Installation

Step 1 — Get the code

Download the source code and place it in your web root (/var/www/ or htdocs).

Step 2 — Install dependencies

cd /var/www/intelis
composer install --no-scripts --no-autoloader --prefer-dist --no-dev
composer dump-autoload -o
composer post-install

The composer post-install command is required after a fresh install.

Step 3 — Set up the database

1. Create a blank database called intelis.
2. Import init.sql from the sql folder into it (e.g., via phpMyAdmin or MySQL CLI).

Step 4 — Configure the application

Copy and edit the configuration file:

cp configs/config.production.dist.php configs/config.production.php

Edit configs/config.production.php:

// Database Settings
$systemConfig['database']['host']     = 'localhost';
$systemConfig['database']['username'] = 'dbuser';
$systemConfig['database']['password'] = 'dbpassword';
$systemConfig['database']['db']       = 'intelis';
$systemConfig['database']['port']     = 3306;
$systemConfig['database']['charset']  = 'utf8mb4';

Enable or disable modules as needed:

// Enable/Disable Modules
$systemConfig['modules']['vl'] = true;              // Viral Load
$systemConfig['modules']['eid'] = true;             // Early Infant Diagnosis
$systemConfig['modules']['covid19'] = false;        // Covid-19
$systemConfig['modules']['generic-tests'] = false;  // Generic Tests
$systemConfig['modules']['hepatitis'] = false;      // Hepatitis
$systemConfig['modules']['tb'] = false;             // Tuberculosis

Step 5 — Set up Apache virtual host

1. Ensure Apache rewrite module is enabled.

2. Add this to /etc/hosts:

   127.0.0.1  intelis.example.org
   

3. Create a virtual host configuration (assuming /var/www/intelis):

   <VirtualHost *:80>
      DocumentRoot "/var/www/intelis/public"
      ServerName intelis.example.org
   
      <Directory "/var/www/intelis/public">
          AddDefaultCharset UTF-8
          Options -Indexes -MultiViews +FollowSymLinks
          AllowOverride All
          Require all granted
      </Directory>
   </VirtualHost>

Need help? See: How to set up Apache Virtual Hosts on Ubuntu

Step 6 — Set up the cron job

sudo EDITOR=gedit crontab -e

Add this line:

* * * * * cd /var/www/intelis/ && ./vendor/bin/crunz schedule:run

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✅ Complete the Setup

Applies to both automated and manual installations.

1. Visit the application in your browser:

   • Manual: Use the hostname you configured (e.g., http://intelis.example.org/)
   • Automated: Use the hostname you chose during setup (default: http://intelis/)

2. Register and set up the admin user.

3. Log in and configure under Admin → System Settings:

   • Sample Types
   • Reasons for Testing
   • Rejection Reasons
   • Users, Provinces, Districts, Facilities
   • Other settings

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🔄 Updating InteLIS

Option 1 — Automated Update (Ubuntu LTS only)

sudo wget -O /usr/local/bin/intelis-update https://github.com/deforay/intelis/raw/master/scripts/upgrade.sh
sudo chmod +x /usr/local/bin/intelis-update
sudo intelis-update

When prompted, enter:

• MySQL password
• STS URL

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Option 2 — Manual Update

1. Pull the latest source or download it manually.

2. Update dependencies:

   cd /var/www/intelis
   composer install --no-scripts --no-autoloader --prefer-dist --no-dev
   composer dump-autoload -o
   composer post-update

   The composer post-update command is required after code updates.

3. Apply any database migrations or config changes (see release notes).

4. Clear cache if needed.

5. Restart Apache:

   sudo systemctl restart apache2

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💬 Support

Need help or commercial licensing?

• Email [email protected]
• Website: https://deforay.com