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Project description
mEdit
Table of Contents
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
PIP
- Make sure
gcc
is installedsudo apt install gcc
- Also make sure your pip up to date
python -m pip install --upgrade pip
- or:
apt install python3-pip
Anaconda
- mEdit utilizes Anaconda to build its own environments under the hood.
- Install Miniconda:
- Download the installer at: https://docs.conda.io/projects/miniconda/en/latest/
bash Miniconda3-latest-<your-OS>.sh
- Set up and update conda:
conda update --all conda config --set channel_priority strict
Mamba
- The officially supported way of installing Mamba is through Miniforge.
- The Miniforge repository holds the minimal installers for Conda and Mamba specific to conda-forge.
- Important:
- The supported way of using Mamba requires that no other packages are installed on the
base
conda environment
- The supported way of using Mamba requires that no other packages are installed on the
- 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
- Important:
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
- In linux systems, install
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
Project details
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