How To Install pyensembl on Ubuntu

Posted on April 1, 2023 (Last modified on May 20, 2023 )

2 minutes • 395 words

Introduction

In this tutorial we learn how to install pyensembl on Ubuntu.

What is `pyensembl`

pyensembl is:

The Ensembl genome database is an established reference for genomic sequences and their automated annotation. To have this data local has advantages for bulk analyses, e.g. for the mapping of reads from RNA-seq against the latest golden path - or a previous one to compare analyses.

This package provides a reproducible way to insatll this data and thus simplify the automation of respective workflows.

There are three methods to install pyensembl on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install pyensembl Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install pyensembl using apt-get by running the following command:

sudo apt-get -y install pyensembl

Install pyensembl Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install pyensembl using apt by running the following command:

sudo apt -y install pyensembl

Install pyensembl Using aptitude

If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install pyensembl using aptitude by running the following command:

sudo aptitude -y install pyensembl

How To Uninstall pyensembl on Ubuntu

To uninstall only the pyensembl package we can use the following command:

sudo apt-get remove pyensembl

Uninstall pyensembl And Its Dependencies

To uninstall pyensembl and its dependencies that are no longer needed by Ubuntu, we can use the command below:

sudo apt-get -y autoremove pyensembl

Remove pyensembl Configurations and Data

To remove pyensembl configuration and data from Ubuntu we can use the following command:

sudo apt-get -y purge pyensembl

Remove pyensembl configuration, data, and all of its dependencies

We can use the following command to remove pyensembl configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge pyensembl

Dependencies

pyensembl have the following dependencies:

References

pyensembl website

Summary

In this tutorial we learn how to install pyensembl package on Ubuntu using different package management tools: apt, apt-get and aptitude.