Installation

For fast resolve of conda package dependencies, we recommend mamba as drop in replacement of conda, simply install mamba into your base conda environment and run commands replacing conda with mamba.

Conda

For details on conda please refer to the conda manual .

Installation should be as easy as running:

conda install -c conda-forge -c bioconda rnamediator

Note

Best practice would be to install into an encapsulated environment via:

conda create -n rnamediator -c conda-forge -c bioconda rnamediator

Pip

Installation via Pip is simple. Just type:

pip install rnamediator

Note

Most of the required packages will be installed. However, the ViennaRNA package needs to be in PATH. Also, make sure that the Python API of the ViennaRNA package is installed.

Parallelization

For distribution of jobs one can either rely on local hardware or use scheduling software like Slurm or the SGE.

This manual will only show examples on local and SLURM usage.