How To Install salmon on Ubuntu 18.04
Introduction
In this tutorial we learn how to install salmon on Ubuntu 18.04.
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 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install 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 18.04
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 18.04, 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 18.04 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
References
Summary
In this tutorial we learn how to install salmon package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
