Connect with us

Software

Installing Snakemake on Ubuntu (Linux)

Published

on

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.

Software

How to calculate binding pocket volume using PyVol plugin in PyMol?

Published

on

How to calculate binding pocket volume using PyVol plugin in PyMol?

Previously, we provided a tutorial for PyVol plugin [1] installation. In this article, we will calculate the binding pocket volume of protein using the same plugin in PyMol [2]. (more…)

Continue Reading

Software

How to generate electron density map using Pymol?

Published

on

How to generate electron density map using Pymol?

Electron density maps are available for most of the protein structures in PDB. Therefore, in this article, we are using PDB to generate electron density maps in Pymol.

(more…)

Continue Reading

Software

Installing PyVOL plugin in Pymol on Ubuntu (Linux).

Published

on

Installing PyVOL plugin in Pymol on Ubuntu (Linux).

PyVOL [1] is an excellent plugin of Pymol [2] for pocket visualization of proteins. In this article, we will install the PyVOL plugin in Pymol on Ubuntu. (more…)

Continue Reading

LATEST ISSUE

ADVERT