Introduction
In this tutorial we learn how to install biobambam2 on Ubuntu 22.04.
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 22.04. 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 22.04
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 22.04, 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 22.04 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 22.04 using different package management tools: apt, apt-get and aptitude.
