Hello! This is the MSA_tool project, where I will be developing the MSA module for the ProteusAI tool developed by @Jonfunk21. The purpose of this project is to design a data pipeline for producing MSA's. This program should recieve as Input a FASTA protein file and outputs an MSA with its respective family protein ID and which conerved residues from this MSA are conserved within the input.
This MSA tool has been tested using Ubuntu 22.04 and MacOS 10.13.6 High sierra. It should therfore work in any linux-based system that has Python installed(Normally built in).
- Python >= 3.8
(older versions may work but have not been tested)
It is recommended that for proper use or installation of the MSA tool Conda is installed and set up a conda environment using the .yml file.
Conda is an open-source package management and environment system which allows easy install, run and update software packages and their respective dependencies. Mini conda is the Conda installer recommended and the one used for this project. Follow the installation instruction in their webpage here
To create a new Conda environment open your terminal and first download the repository and enter the project:
git clone https://github.com/CoditoDTU/MSA_tool
cd path/to/MSA_tool
Afterwards, you can create the Conda environment using the environment.yml file which has every package and dependency you need. The name of the environment created will be "msa_tool".
conda env create -f environment.yml
conda activate msa_tool
To check wether you are in the correct environment you can use the following command:
conda env list
This will show you the list of all your environments and show you which are you currently using denoted by an (*).
While trying to run bash scripts your equipment may not run without the proper activation of the files. Therefore, in order to make them executable follow the next commands:
chmod u+x your_bash_file.sh # Makes the file executable
./your_bash_file.sh <PLACEHOLDER_ARGUMENTS> # Runs the executable .sh files