ChromHMM command not found

Introduction

When you run more command in linux terminal / console, you get the following error message

ChromHMM: command not found

or when using sudo you get the following error message

sudo: ChromHMM: command not found

Solutions to ChromHMM: command not found

How To Fix ChromHMM: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu ChromHMM is provided by chromhmm package.

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.

To fix this problem, we can install more using the command below.

sudo apt-get -y install chromhmm

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install chromhmm.

sudo apt -y install chromhmm

Or if you have aptitude installed you can use the following command.

sudo aptitude install chromhmm

Summary

In this tutorial we learn how to fix ChromHMM command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.