How To Install pycoqc on Ubuntu

Posted on April 1, 2023 (Last modified on May 20, 2023 )

2 minutes • 393 words

Introduction

In this tutorial we learn how to install pycoqc on Ubuntu.

What is `pycoqc`

pycoqc is:

PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data

PycoQC relies on the sequencing_summary.txt file generated by Albacore and Guppy, but if needed it can also generates a summary file from basecalled fast5 files. The package supports 1D and 1D2 runs generated with Minion, Gridion and Promethion devices and basecalled with Albacore 1.2.1+ or Guppy 2.1.3+

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

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

sudo apt-get update

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

sudo apt-get -y install pycoqc

Install pycoqc Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install pycoqc

Install pycoqc 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 pycoqc using aptitude by running the following command:

sudo aptitude -y install pycoqc

How To Uninstall pycoqc on Ubuntu

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

sudo apt-get remove pycoqc

Uninstall pycoqc And Its Dependencies

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

sudo apt-get -y autoremove pycoqc

Remove pycoqc Configurations and Data

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

sudo apt-get -y purge pycoqc

Remove pycoqc configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge pycoqc

Dependencies

pycoqc have the following dependencies:

References

pycoqc website

Summary

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