How To Install python-pbgenomicconsensus on Debian 9

In this tutorial we learn how to install python-pbgenomicconsensus on Debian 9. python-pbgenomicconsensus is Pacific Biosciences variant and consensus caller (Python 2)

Introduction

In this tutorial we learn how to install python-pbgenomicconsensus on Debian 9.

What is python-pbgenomicconsensus

python-pbgenomicconsensus is:

The GenomicConsensus package provides Quiver, Pacific Biosciences' flagship consensus and variant caller. Quiver is an algorithm that finds the maximum likelihood template sequence given PacBio reads of the template. These reads are modeled using a conditional random field approach that prescribes a probability to a read given a template sequence. In addition to the base sequence of each read, Quiver uses several additional quality value covariates that the base caller provides.

This package is part of the SMRTAnalysis suite and provides the Python 2 backend library.

There are three methods to install python-pbgenomicconsensus on Debian 9. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install python-pbgenomicconsensus Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install python-pbgenomicconsensus

Install python-pbgenomicconsensus Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install python-pbgenomicconsensus

Install python-pbgenomicconsensus 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 Debian. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install python-pbgenomicconsensus using aptitude by running the following command:

sudo aptitude -y install python-pbgenomicconsensus

How To Uninstall python-pbgenomicconsensus on Debian 9

To uninstall only the python-pbgenomicconsensus package we can use the following command:

sudo apt-get remove python-pbgenomicconsensus

Uninstall python-pbgenomicconsensus And Its Dependencies

To uninstall python-pbgenomicconsensus and its dependencies that are no longer needed by Debian 9, we can use the command below:

sudo apt-get -y autoremove python-pbgenomicconsensus

Remove python-pbgenomicconsensus Configurations and Data

To remove python-pbgenomicconsensus configuration and data from Debian 9 we can use the following command:

sudo apt-get -y purge python-pbgenomicconsensus

Remove python-pbgenomicconsensus configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge python-pbgenomicconsensus

Dependencies

python-pbgenomicconsensus have the following dependencies:

References

Summary

In this tutorial we learn how to install python-pbgenomicconsensus package on Debian 9 using different package management tools: apt, apt-get and aptitude.