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Installing Snakemake on Ubuntu (Linux)

Tariq Abdullah

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Installing Snakemake on Ubuntu (Linux)

Snakemake is a workflow management system to create scalable data analyses [1]. Workflows are defined in Python-based language. In this article, we are going to install Snakemake on Ubuntu (Linux).

Preparing system

Open a terminal by pressing Ctrl+Alt+T. Update and upgrade your system using the following commands:

$ sudo apt-get update

$ sudo apt-get upgrade

Installing prerequisites

Before installing Snakemake, you need to install Conda and Mamba. To install Conda, read this article.

Installing Mamba

In the terminal, paste the following command.

$ conda install mamba -n base -c conda-forge

It will take some time to finish.

Installing Snakemake

Paste the following commands in the terminal.

$ conda activate base

$ mamba create -c conda-forge -c bioconda -n snakemake snakemake

It will start downloading the required packages.

After a successful downloading and installation, paste the following command.

$ conda activate snakemake

Now check the installation by running the following command

$ snakemake --help

It should display usage.


References

  1. Mölder, F., Jablonski, K. P., Letcher, B., Hall, M. B., Tomkins-Tinch, C. H., Sochat, V., … & Köster, J. (2021). Sustainable data analysis with Snakemake. F1000Research10.

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

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