How To Install pbbamtools on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 406 words
Introduction
In this tutorial we learn how to install pbbamtools on Ubuntu.
What is pbbamtools
pbbamtools is:
The BAM format is a binary, compressed, record-oriented container format for raw or aligned sequence reads. The associated SAM format is a text representation of the same data. The specifications for BAM/SAM are maintained by the SAM/BAM Format Specification Working Group.
PacBio-produced BAM files are fully compatible with the BAM specification, but makes use of the extensibility mechanisms of the BAM specification to encode PacBio-specific information.
This package provides command-line utilities for working with PacBio BAM files.
There are three methods to install pbbamtools 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 pbbamtools Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install pbbamtools using apt-get by running the following command:
sudo apt-get -y install pbbamtools
Install pbbamtools Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install pbbamtools using apt by running the following command:
sudo apt -y install pbbamtools
Install pbbamtools 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 pbbamtools using aptitude by running the following command:
sudo aptitude -y install pbbamtools
How To Uninstall pbbamtools on Ubuntu
To uninstall only the pbbamtools package we can use the following command:
sudo apt-get remove pbbamtools
Uninstall pbbamtools And Its Dependencies
To uninstall pbbamtools and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove pbbamtools
Remove pbbamtools Configurations and Data
To remove pbbamtools configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge pbbamtools
Remove pbbamtools configuration, data, and all of its dependencies
We can use the following command to remove pbbamtools configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge pbbamtools
Dependencies
pbbamtools have the following dependencies:
References
Summary
In this tutorial we learn how to install pbbamtools package on Ubuntu using different package management tools: apt, apt-get and aptitude.