htsfile command not found

Introduction

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

htsfile: command not found

or when using sudo you get the following error message

sudo: htsfile: command not found

Solutions to htsfile: command not found

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

In Ubuntu htsfile is provided by tabix package.

tabix is:

Tabix indexes files where some columns indicate sequence coordinates: name (usually a chromosome), start and stop. The input data file must be position sorted and compressed by bgzip (provided in this package), which has a gzip like interface. After indexing, tabix is able to quickly retrieve data lines by chromosomal coordinates. Fast data retrieval also works over network if an URI is given as a file name.

This package is built from the HTSlib source, and provides the bgzip, htsfile, and tabix tools.

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

sudo apt-get -y install tabix

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

You can also use apt command to install tabix.

sudo apt -y install tabix

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

sudo aptitude install tabix

Summary

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