How To Install biobambam2 on Ubuntu 20.04

In this tutorial we learn how to install biobambam2 on Ubuntu 20.04. biobambam2 is tools for early stage alignment file processing

Introduction

In this tutorial we learn how to install biobambam2 on Ubuntu 20.04.

What is biobambam2

biobambam2 is:

This package contains some tools for processing BAM files including

bamsormadup: parallel sorting and duplicate marking bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading. bamsort: reads BAM and writes BAM resorted by coordinates or query name bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name

There are three methods to install biobambam2 on Ubuntu 20.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install biobambam2 Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install biobambam2 using apt-get by running the following command:

sudo apt-get -y install biobambam2

Install biobambam2 Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install biobambam2 using apt by running the following command:

sudo apt -y install biobambam2

Install biobambam2 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 biobambam2 using aptitude by running the following command:

sudo aptitude -y install biobambam2

How To Uninstall biobambam2 on Ubuntu 20.04

To uninstall only the biobambam2 package we can use the following command:

sudo apt-get remove biobambam2

Uninstall biobambam2 And Its Dependencies

To uninstall biobambam2 and its dependencies that are no longer needed by Ubuntu 20.04, we can use the command below:

sudo apt-get -y autoremove biobambam2

Remove biobambam2 Configurations and Data

To remove biobambam2 configuration and data from Ubuntu 20.04 we can use the following command:

sudo apt-get -y purge biobambam2

Remove biobambam2 configuration, data, and all of its dependencies

We can use the following command to remove biobambam2 configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge biobambam2

References

Summary

In this tutorial we learn how to install biobambam2 package on Ubuntu 20.04 using different package management tools: apt, apt-get and aptitude.