rendrick27/alignevaluator

Comparison of alignment software

Description

This tool, developed within the scope of Laboratório de Bioinformática, aims to compare alignment software (MAFFT, Clustal, and Muscle) through p-SH and p-AU tests using IQTree.

Requisites

• At least one FASTA file in the folder dataset;
• Docker;
• Docker Desktop (Opcional)
• Acess to internet (Only when installing the app)

Installation

Download and Extract Project from GitLab

# Download the project from GitLab
wget https://gitlab.com/laboratorio-de-bioinformatica-2023-2024/sorting-hat/-/archive/main/sorting-hat-main.zip

# Unzip the folder
unzip sorting-hat-main.zip

# Navigate to the Snakemake directory
cd sorting-hat-main

Alternatively, Pull Docker Image from Docker Hub

# Pull the Docker image from Docker Hub
docker pull rendrick27/snakemake

Usage

If you haven't pulled the image from Docker Hub, execute the following commands inside the sorting-hat-main folder:

docker build -t {image_name} .

docker run -it --name {container_name} {image_name} /bin/bash

Then, run the following command:

snakemake --use-conda all --cores all

Saving Results

To save files from the Docker container, use the following commands:

# Identify Containers
docker ps -a

# Stop Containers
docker stop <container_id>

# Export container files to desktop
docker export <container_id> > ~/Desktop/container_<container_name>.tar

Alternatively, you can use Docker Desktop to save files on your desktop by navigating to Docker Desktop > Containers > Actions > View Files. Select the files you want and click "Save".

Settings

You may adjust settings in the Snakemake command, such as threads and bootstraps, but remember that using more threads may cause more issues.

Credits

Rendrick Carreira - 201901365

License

MIT License