How To Install chromhmm on Ubuntu 22.04

In this tutorial we learn how to install chromhmm on Ubuntu 22.04. chromhmm is Chromatin state discovery and characterization

Introduction

In this tutorial we learn how to install chromhmm on Ubuntu 22.04.

What is chromhmm

chromhmm is:

ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial patterns of marks. ChromHMM is based on a multivariate Hidden Markov Model that explicitly models the presence or absence of each chromatin mark. The resulting model can then be used to systematically annotate a genome in one or more cell types. By automatically computing state enrichments for large-scale functional and annotation datasets ChromHMM facilitates the biological characterization of each state. ChromHMM also produces files with genome-wide maps of chromatin state annotations that can be directly visualized in a genome browser.

There are three methods to install chromhmm on Ubuntu 22.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install chromhmm Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install chromhmm

Install chromhmm Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install chromhmm

Install chromhmm 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 chromhmm using aptitude by running the following command:

sudo aptitude -y install chromhmm

How To Uninstall chromhmm on Ubuntu 22.04

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

sudo apt-get remove chromhmm

Uninstall chromhmm And Its Dependencies

To uninstall chromhmm and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:

sudo apt-get -y autoremove chromhmm

Remove chromhmm Configurations and Data

To remove chromhmm configuration and data from Ubuntu 22.04 we can use the following command:

sudo apt-get -y purge chromhmm

Remove chromhmm configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge chromhmm

References

Summary

In this tutorial we learn how to install chromhmm package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.