How To Install yanosim on Ubuntu

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

2 minutes  • 421 words

Introduction

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

What is yanosim

yanosim is:

Yanosim has three options:

1. yanosim model: Creates an model of mismatches, insertions and deletions based on an alignment of nanopore DRS reads to a reference. Reads should be aligned to a transcriptome i.e. without spliced alignment, using minimap2. They should have the cs tag.
2. yanosim quantify: Quantify the number of reads mapping to each transcript in a reference, so that the right number of reads can be simulated.
3. yanosim simulate: Given a model created using yanosim model, and per-transcript read counts created using yanosim simulate, simulate error-prone long-reads from the given fasta file.

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

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

sudo apt-get update

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

sudo apt-get -y install yanosim

Install yanosim Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install yanosim

Install yanosim 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 yanosim using aptitude by running the following command:

sudo aptitude -y install yanosim

How To Uninstall yanosim on Ubuntu

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

sudo apt-get remove yanosim

Uninstall yanosim And Its Dependencies

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

sudo apt-get -y autoremove yanosim

Remove yanosim Configurations and Data

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

sudo apt-get -y purge yanosim

Remove yanosim configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge yanosim

Dependencies

yanosim have the following dependencies:

• python3-click
• python3-numpy
• python3-pysam
• python3-scipy
• python3

References

• yanosim website

Summary

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