How To Install salmon on Ubuntu

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

3 minutes • 448 words

Introduction

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

What is `salmon`

salmon is:

Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves is accuracy and speed via a number of different innovations, including the use of lightweight alignments (accurate but fast-to-compute proxies for traditional read alignments) and massively-parallel stochastic collapsed variational inference. The result is a versatile tool that fits nicely into many different pipelines. For example, you can choose to make use of the lightweight alignments by providing Salmon with raw sequencing reads, or, if it is more convenient, you can provide Salmon with regular alignments (e.g. computed with your favorite aligner), and it will use the same wicked-fast, state-of-the-art inference algorithm to estimate transcript-level abundances for your experiment.

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

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

sudo apt-get update

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

sudo apt-get -y install salmon

Install salmon Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install salmon

Install salmon 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 salmon using aptitude by running the following command:

sudo aptitude -y install salmon

How To Uninstall salmon on Ubuntu

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

sudo apt-get remove salmon

Uninstall salmon And Its Dependencies

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

sudo apt-get -y autoremove salmon

Remove salmon Configurations and Data

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

sudo apt-get -y purge salmon

Remove salmon configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge salmon

Dependencies

salmon have the following dependencies:

References

salmon website

Summary

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