alleleCounterToJson.pl command not found

Introduction

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

alleleCounterToJson.pl: command not found

or when using sudo you get the following error message

sudo: alleleCounterToJson.pl: command not found

Solutions to alleleCounterToJson.pl: command not found

How To Fix alleleCounterToJson.pl: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu alleleCounterToJson.pl is provided by liballelecount-perl package.

liballelecount-perl is:

Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings).

The alleleCount package primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenberg.

This package provided the Perl interface to alleleCounter providing Sanger::CGP::AlleleCount::Genotype.

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

sudo apt-get -y install liballelecount-perl

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

You can also use apt command to install liballelecount-perl.

sudo apt -y install liballelecount-perl

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

sudo aptitude install liballelecount-perl

Summary

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