How To Install ea-utils on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 474 words
Introduction
In this tutorial we learn how to install ea-utils on Ubuntu.
What is ea-utils
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.
There are three methods to install ea-utils on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install ea-utils Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install ea-utils using apt-get by running the following command:
sudo apt-get -y install ea-utils
Install ea-utils Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install ea-utils using apt by running the following command:
sudo apt -y install ea-utils
Install ea-utils Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install ea-utils using aptitude by running the following command:
sudo aptitude -y install ea-utils
How To Uninstall ea-utils on Ubuntu
To uninstall only the ea-utils package we can use the following command:
sudo apt-get remove ea-utils
Uninstall ea-utils And Its Dependencies
To uninstall ea-utils and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove ea-utils
Remove ea-utils Configurations and Data
To remove ea-utils configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge ea-utils
Remove ea-utils configuration, data, and all of its dependencies
We can use the following command to remove ea-utils configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge ea-utils
Dependencies
ea-utils have the following dependencies:
References
Summary
In this tutorial we learn how to install ea-utils package on Ubuntu using different package management tools: apt, apt-get and aptitude.