How To Install biobambam2 on Kali Linux
Introduction
In this tutorial we learn how to install biobambam2 on Kali Linux.
What is biobambam2
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 ways to install biobambam2 on Kali Linux . 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 Kali Linux. 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 Kali Linux
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 Kali Linux, we can use the command below:
sudo apt-get -y autoremove biobambam2
Remove biobambam2 Configurations and Data
To remove biobambam2 configuration and data from Kali Linux 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 using different package management tools like apt, apt-get and aptitude.