meditability 0.2.4

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mEdit

Table of Contents

• What is mEdit?
  • Program Structure
  • Features
• Getting Started
  • Prerequisites
  • Installation
  • Running Tests
• Usage
• Roadmap
• Contributing
• FAQ
• License
• Contact

What is mEdit?

Program Structure

Features

• Reference Human Genome
  • mEdit has three different options for loading reference genomes:
  • 1- The latest compatible reference used by the HPRC on human pangenome assemblies
  • 2- The latest RefSeq human genome reference
  • 3- Custom version provided by the user

Getting Started

Prerequisites

• The current version has 4 prerequisites:
  • PIP
  • Anaconda
  • Mamba
  • AWS-CLI
  • Tabix

PIP

• Make sure gcc is installed

  sudo apt install gcc
  

• Make sure your pip up to date

  python -m pip install --upgrade pip
  

  • or:

  apt install python3-pip
  

Anaconda

• Install Miniconda:
  • Download the installer at: https://docs.conda.io/projects/miniconda/en/latest/

  bash Miniconda3-latest-<your-OS>.sh
  

• Set up your conda environment:

  conda update --all
  conda config --set channel_priority strict
  

Mamba

• The officially supported way of installing Mamba is through Miniforge.
  • Important:
    • The supported way of using Mamba requires that no other packages are installed on the base conda environment
  • More information about miniforge: https://github.com/conda-forge/miniforge
  • Details on how to correctly install Mamba: https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html

    wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge-pypy3-<your-OS>.sh
    bash Miniforge-pypy3-<your-OS>.sh
    

AWS CLI

• Make sure you are signed in with your AWS credentials:
• More information: https://docs.aws.amazon.com/cli/latest/userguide/getting-started-install.html

  curl "https://awscli.amazonaws.com/awscli-exe-<your-OS>.zip" -o "awscliv2.zip"
  unzip awscliv2.zip
  sudo ./aws/install 
  

Tabix

• This allows mEdit to use bgzip for file compression.
  • In linux systems, install tabix.

      apt install tabix
    

  • On macOS machines, intall htslib.

      brew install htslib
    

Installation

mEdit is compatible with UNIX-based systems running on Intel processors and it's conveniently available via pyPI:

pip install meditability

Running Tests

Usage

• db_set
• list
• guide_prediction
• offtargets

Roadmap

Contributing

FAQ

License

Contact