Apscale Installer

Important changes

• BOLDigger3 is now implement in Apscale-GUI [30.10.2024]
• The environment is now called "apscale" instead of "metabarcoding" [30.10.2024]

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
• Demultiplexer
• 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. Ensure you provide the correct path, for example:

   conda env create -f /Users/tillmacher/Downloads/apscale_env_windows_aarch64.yml
   

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

   conda activate apscale
   

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

   apscale_installer
   

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

   conda install vsearch
   conda install blast
   playwright install
   

9. Verify your installations:

   vsearch --help
   blastn -h
   

• If you want to update the metabarcoding environment type:

  conda env update --file apscale_env_windows_aarch64.yml --prune
  

• If you want to uninstall the metabarcoding environment type:

  conda remove -n apscale --all
  

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
• Demultiplexer
• TaxonTableTool2 (coming soon)

Video tutorial

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