Installing eukrhythmic

eukrhythmic is designed as a modular pipeline that you can fully customize as the user of the resource. As such, we recommend setting up the base environment provided in the environment.yaml file prior to running anything.

Downloading eukrhythmic

You may download the pipeline by cloning it directly from GitHub.:

git clone https://github.com/AlexanderLabWHOI/eukrhythmic
cd eukrhythmic

All eukrhythmic commands are run from the base directory.

If you want to receive further information or plan on executing from the command line, go ahead and run:

alias eukrhythmic='./bin/eukrhythmic.sh'

Then, you can execute eukrhythmic -h to see that the software is present in the workspace.

Refer to “Running the pipeline from the command line” for more information on using command-line arguments with eukrhythmic.

We note that most of our documentation on the use of a scheduler to run eukrhythmic in parallel on multiple machines is written for the SLURM scheduling system. We provide some documentation on the use of the PBS system in the “Using eukrhythmic” section, but invite you to submit an issue on our GitHub page if you would like guidance on how to use PBS or an alternative system to run the pipeline.

Setting up a conda environment for running Snakemake

Initialize the pipeline by setting up a conda environment, such that all the requested packages are loaded.:

conda env create eukrhythmic --file environment.yaml

If this doesn’t work for you, please try to set a conda environment manually that contains Snakemake, preferably newer than version 6, Python, preferably newer than version 3.8, mamba, some version of pandas and some version of pyyaml.