Alcazar Biostore on Linux

This article describes how to deploy Alcazar Biostore on Linux. It is not meant to be a comprehensive manual, but rather a quick start guide to get you up and running, pointing out key steps and considerations.

This guide is based on the Debian 12 distribution, but the steps should be similar for other Linux distributions.

Prerequisites

• A Linux server with a supported distribution (this guide is based on Debian 12)

Install the .NET SDK

To run Alcazar Biostore, you need to have the .NET 8.0 runtime installed on your Linux server.

1. Get Microsoft packages

   wget https://packages.microsoft.com/config/debian/12/packages-microsoft-prod.deb -O packages-microsoft-prod.deb
   sudo dpkg -i packages-microsoft-prod.deb
   rm packages-microsoft-prod.deb
   

2. Install ASP.NET Core runtime

   sudo apt update
   sudo apt install aspnetcore-runtime-8.0
   

3. Update and upgrade

   sudo apt-get update
   sudo apt-get upgrade
   

See https://learn.microsoft.com/en-us/dotnet/core/install/linux-debian?tabs=dotnet8 for a more comprehensive guide on installing the .NET SDK on Debian.

Install Alcazar Biostore

1. Copy the application deployment packages to the server.
2. Unzip the packages to a folder, typically /var/www/Alcazar/Biostore, or /var/www/Alcazar/Biostore.Agent.

unzip filename.zip

Required changes

Change	Windows	Linux	Remarks
Configuration folder	c:/ProgramData/Alcazar/Biostore	/usr/share/Alcazar/Biostore	No action required, the runtime sets the correct folder.
Log folders in NLog configuration	c:/ProgramData/Alcazar/Biostore/logs	/usr/share/Alcazar/Biostore/logs	Manually change the NLog configuration file in the installation folder AND in /usr/share/Alcazar/Biostore/conf accordingly. If the NLog files are not changed, log files are created under the installation folder starting with C:
wwwroot	-	-	Manually create the wwwroot folder in the installation folder, if not present, to avoid a warning message when starting the application.
HTTP and HTTPS ports	Handled by IIS	appsettings.json Kestrel section	Manually edit appsettings.json tp specify the HTTP and HTTPS ports, else dotnet will randomly select ports.

appsettings.json

Edit appsettings.json to specify the HTTP and HTTPS ports.

"Kestrel": {
  "Endpoints": {
    "Https": {
      "Url": "https://*:443"
    },
    "Http": {
      "Url": "http://*:8080"
    }
  }
}

Host on the Kestrel server

To host the application on the Kestrel server, you can use the dotnet command to run the application.

dotnet /var/www/Alcazar/Biostore/Alcazar.Biostore.dll

You can also create a systemd service to run the application as a background service.

Nginx as reverse proxy

TBS

Known issues

Issue	Remarks
None

Kubernetes

Logging

• Log files will be at /usr/share/Alcazar/Biostore/logs inside the container, but they are not persisted across container restarts.
• To persist or access them, mount a Kubernetes volume to that path.