How To Install bcalm on Ubuntu 20.04

In this tutorial we learn how to install bcalm on Ubuntu 20.04. bcalm is de Bruijn compaction in low memory

Introduction

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

What is bcalm

bcalm is:

A bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data.

This is the parallel version of the BCALM software using gatb-core library.

There are three methods to install bcalm 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 bcalm Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install bcalm

Install bcalm Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install bcalm

Install bcalm 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 bcalm using aptitude by running the following command:

sudo aptitude -y install bcalm

How To Uninstall bcalm on Ubuntu 20.04

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

sudo apt-get remove bcalm

Uninstall bcalm And Its Dependencies

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

sudo apt-get -y autoremove bcalm

Remove bcalm Configurations and Data

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

sudo apt-get -y purge bcalm

Remove bcalm configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge bcalm

References

Summary

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