/oligo_miner_env

A conda environment for running OligoMiner

OligoMinerEnv

A conda environment for running OligoMiner code.

Installation and usage

  1. Install conda

  2. Clone this repo. Create and activate the conda environment:

$ git clone https://github.com/conorcamplisson/oligo_miner_env.git && cd oligo_miner_env/
$ conda env create -f environment.yml
$ conda activate oligo_miner_env
  1. That's it! Now you can run OligoMiner:
$ git clone https://github.com/brianbeliveau/OligoMiner.git && cd OligoMiner/
$ python probeTm.py -i TATGAGGACGAATCTCCCGCTTATA
32.85

Background

OligoMiner requires several python and non-python dependencies:

  • python 2.7
  • biopython
  • scikit-learn
  • bowtie2
  • jellyfish
  • NUPACK

The environment and package manager conda makes the install process easy, and this repository provides a conda environment that is sufficient to run OligoMiner on Linux and MacOS. Windows users should enable Ubuntu for Windows 10--a complete Linux operating system--and then follow instructions for Linux users.