ORFmine - Installation Guide#

A comprehensive guide to installing and running ORFmine.

Requirements#

To get started, you will need:

  • Python 3.9 (or 3.10)
  • pip
  • Either Docker or Singularity (Apptainer)

Python Setup#

Check if Python 3.9 or 3.10 is already available on your system.

  • Already installed ? Go to Installation Options

  • Not installed ? follow one of the options below to create isolated python environment.

Option A – Using virtualenv#

   python3.9 -m pip install --upgrade pip
   python3.9 -m pip install virtualenv

   # Create environment
   virtualenv env-3.9

   # Activate python environment 
   source env-3.9/bin/activate

   # To deactivate the environment:
   deactivate

Option B – Using Conda#

   # Create conda environment
   conda create --name env_python3.9 python=3.9

   # To activate the environement: 
   conda activate env_python3.9

Installation Options#

ORFmine can be installed in several ways. Choose the option that best suits your needs: It will install the last version of orfmine

Option 1 : From Pypi (Recommanded):#

    pip install orfmine

Option 2: From a Local Repository#

  1. Clone the ORFmine repository: 
    git clone https://github.com/i2bc/ORFmine.git
  1. Navigate to the cloned directory: 
    cd ORFmine
  1. Install ORFmine in editable mode: 
    python3 -m pip install --upgrade pip
    python3 -m pip install -e .

ORFmine relies on a suite of external tools in addition to its core Python scripts. The commands above only install the Python components and a few dependencies. To ensure full functionality, including access to all required third-party software, you must complete the installation using the containerized environment provided (via Docker or Singularity). This guarantees a fully configured, portable, and reproducible setup.Docker and Singularity build

Note: Regardless of the installation method you choose, you must install the following tool to use ORFold:

   pip install git+https://github.com/T-B-F/pyHCA.git

Docker and Singularity build#

For containerized environments, ORFmine supports Docker and Singularity. Make sure to have docker or singularity installed in your machine before building the image. For Docker, make sure you have root permissions.

  • Docker: 
    docker pull fadwa06/orfmine:3.0.1
  • Singularity (or Apptainer): 
   singularity build orfmine_latest.sif docker://fadwa06/orfmine:3.0.1

License#

ORFmine is licensed under the MIT License. For more details, see the LICENSE file.

Citation#

If you use ORFmine in your research, please cite the following papers:

Papadopoulos, C., Chevrollier, N., Lopes, A. Exploring the peptide potential of genomes. Meth. Mol. Biol. (2022)
Papadopoulos, C., Arbes, H., Chevrollier, N., Blanchet, S., Cornu, D., Roginski, P., Rabier, C., Atia, S., Lespinet, O., Namy, O., Lopes, A. The Ribosome Profiling landscape of yeast reveals a high diversity in pervasive translation. bioRxiv (2023)