How To Install chromhmm on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 440 words
Introduction
In this tutorial we learn how to install chromhmm on Ubuntu.
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. 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
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, 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 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
Dependencies
chromhmm have the following dependencies:
References
Summary
In this tutorial we learn how to install chromhmm package on Ubuntu using different package management tools: apt, apt-get and aptitude.