bamclipper.sh command not found

In this troubleshooting guide we learn how to fix bamclipper.sh command not found error message

Introduction

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

bamclipper.sh: command not found

or when using sudo you get the following error message

sudo: bamclipper.sh: command not found

In Ubuntu bamclipper.sh is provided by bamclipper package.

bamclipper is:

Remove gene-specific primer sequences from SAM/BAM alignments of PCR amplicons by soft-clipping.

bamclipper.sh soft-clips gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.

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

sudo apt-get -y install bamclipper

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

You can also use apt command to install bamclipper.

sudo apt -y install bamclipper

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

sudo aptitude install bamclipper

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