ea-alc command not found

In this troubleshooting guide we learn how to fix ea-alc command not found error message

Introduction

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

ea-alc: command not found

or when using sudo you get the following error message

sudo: ea-alc: command not found

In Ubuntu ea-alc is provided by ea-utils package.

ea-utils is:

Ea-utils provides a set of command-line tools for processing biological sequencing data, barcode demultiplexing, adapter trimming, etc.

Primarily written to support an Illumina based pipeline - but should work with any FASTQs.

Main Tools are:

fastq-mcf Scans a sequence file for adapters, and, based on a log-scaled threshold, determines a set of clipping parameters and performs clipping. Also does skewing detection and quality filtering.
fastq-multx Demultiplexes a fastq. Capable of auto-determining barcode id’s based on a master set fields. Keeps multiple reads in-sync during demultiplexing. Can verify that the reads are in-sync as well, and fail if they’re not.
fastq-join Similar to audy’s stitch program, but in C, more efficient and supports some automatic benchmarking and tuning. It uses the same “squared distance for anchored alignment” as other tools.
varcall Takes a pileup and calculates variants in a more easily parameterized manner than some other tools.

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

sudo apt-get -y install ea-utils

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

You can also use apt command to install ea-utils.

sudo apt -y install ea-utils

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

sudo aptitude install ea-utils

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