Metadata-Version: 2.1
Name: apscale_installer
Version: 0.4
Summary: Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data - Conda installer (workaround)
Home-page: https://pypi.org/project/apscale_installer/
Author: Till-Hendrik Macher
Author-email: macher@uni-trier.de
License: MIT
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: Requests==2.32.3

# Apscale Installer

## Installation Tutorial for the Apscale Metabarcoding Workflow

## Introduction

The easiest way to install the apscale metabarcoding workflow is by using [Miniconda3](https://docs.anaconda.com/miniconda/#). Miniconda will create an isolated environment with all the suggested versions of each tool.

> **Note:** Currently, [vsearch](https://github.com/torognes/vsearch) and [blast+](https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html) 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](https://github.com/DominikBuchner/apscale)
* [Apscale-GUI](https://github.com/TillMacher/apscale_gui)
* [Apscale_blast](https://github.com/TillMacher/apscale_blast)
* [Boldigger2](https://github.com/DominikBuchner/BOLDigger2)
* [Demultiplexer](https://github.com/DominikBuchner/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](https://github.com/TillMacher/apscale_installer/blob/main/environments/metabarcoding_env_windows_x64.yml) or [MacOS](https://github.com/TillMacher/apscale_installer/blob/main/environments/metabarcoding_env_macos_aarch64.yml).

4. Install the metabarcoding environment by typing:
   ```sh
   conda env create -f metabarcoding_env_XXX.yml
   
5. Ensure you provide the correct path, for example:
   ```sh
   conda env create -f /Users/tillmacher/Downloads/metabarcoding_env_macos_aarch64.yml
   
6. This should automatically install all dependencies. After the installation, activate the environment:
   ```sh
   conda activate metabarcoding

7. **Windows and MacOS** users run the apscale-installer script:
   ```sh
   apscale_installer

8. **Linux and MacOS (intel)** users can use conda:
   ```sh
   conda install vsearch
   conda install blast

9. Verify your installations:
   ```sh
   vsearch --help
   blastn -h

* If you want to update the metabarcoding environment type:
  ```sh
  conda env update --file metabarcoding_env_XXX.yml --prune

* If you want to uninstall the metabarcoding environment type:
  ```sh
  conda remove -n metabarcoding --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](https://github.com/DominikBuchner/apscale/tree/main?tab=readme-ov-file#how-to-use)
* [Apscale-GUI](https://github.com/TillMacher/apscale_gui)
* [Apscale_blast](https://github.com/TillMacher/apscale_blast?tab=readme-ov-file#how-to-use)
* [Boldigger2](https://github.com/DominikBuchner/BOLDigger2?tab=readme-ov-file#installation-and-usage)
* [Demultiplexer](https://github.com/DominikBuchner/demultiplexer?tab=readme-ov-file#how-to-use)
* TaxonTableTool2 (coming soon)

## Video tutorial
There is also a [YouTube tutorial](https://www.youtube.com/watch?v=c6pm0FhcINI) available, where the installation of **Windows** and **MacOS** is demonstrated.

