OligoMinerEnv
A conda environment for running OligoMiner code.
Installation and usage
-
Install conda
-
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
- 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.