Apscale Installer

Important changes

• APSCALE4 is now implement in APSCALE-GUI [22.08.2025]
• Please update the environment to "apscale4" (upgraded to python3.12)
• The original "apscale" environment is outdated (python3.10 is no longer supported).

Introduction

The easiest way to install the apscale metabarcoding workflow is by using Miniconda3. Miniconda will create an isolated environment with all the suggested versions of each tool.

Note: Currently, vsearch and blast+ cannot be automatically installed via conda. For now, the easiest solution is the installation through the apscale-installer script. We will update this Wiki when vsearch and blast+ are available via conda. Linux users can install vsearch and blast+ already now using conda.

This tutorial will install the following tools:

• Apscale
• Apscale-GUI
• Apscale_blast
• Boldigger3
• Demultiplexer2
• TaxonTableTool2 (coming soon)

Miniconda Installation

1. Install Miniconda by following the instructions.

2. Open a new Anaconda (Miniconda3) terminal.

   • Windows: Type 'Anaconda' in your search bar and select 'Anaconda Powershell Prompt (miniconda3)'.
   • MacOS: Open a new terminal. You will see the (base) environment before your user name.

3. Download the respective environment installation file for Windows or MacOS.

4. Install the metabarcoding environment by typing:

   conda env create -f apscale_env_windows_aarch64.yml
   

5. This should automatically install all dependencies. After the installation, activate the environment:

   conda activate apscale4
   

6. Windows and MacOS users run the apscale-installer script:

   apscale_installer
   

7. Linux and MacOS (intel) users can use conda:

   conda install bioconda::vsearch
   conda install bioconda::blast
   playwright install
   

8. Verify your installations:

   vsearch --help
   blastn -h
   

• If you want to uninstall the old apscale environment type:

  conda remove -n apscale --all
  

Miniconda Installation (manual)

• If the yml installation of the environment fails a manual installation can be performed:

  conda create -n apscale4 python=3.12 ipython
  conda activate apscale4
  pip install apscale
  pip install apscale_gui
  pip install apscale_installer
  pip install apscale_blast
  pip install boldigger3
  pip install demultiplexer2
  apscale_installer
  

Usage

Now that everything is installed, you can use the installed software.

Refer to the homepages of each program to run learn how to use them:

• Apscale
• Apscale-GUI
• Apscale_blast
• Boldigger3
• Demultiplexer2
• TaxonTableTool2 (coming soon)

Video tutorial

There is also a YouTube tutorial available, where the installation of Windows and MacOS is demonstrated.