How To Install rapmap on Ubuntu 18.04
Introduction
In this tutorial we learn how to install rapmap on Ubuntu 18.04.
What is rapmap
rapmap is:
RapMap is a testing ground for ideas in quasi-mapping / (lightweight / pseudo) transcriptome alignment. That means that, at this point, it is somewhat experimental. The develop branch will have the latest improvements and additions, but is not guaranteed to be stable between commits. Breaking changes to the master branch will be accompanied by a tag to the version before the breaking change. Currently, RapMap is a stand-alone quasi-mapper that can be used with other tools. It is also being used as part of Sailfish and Salmon. Eventually, the hope is to create and stabilize an API so that it can be used as a library from other tools.
Quasi-mapping / (lightweight / pseudo)-alignment is the term that is used here for the type of information required for certain tasks (e.g. transcript quantification) that is less “heavyweight” than what is provided by traditional alignment. For example, one may only need to know the transcripts / contigs to which a read aligns and, perhaps, the position within those transcripts rather than the optimal alignment and base-for-base CIGAR string that aligns the read and substring of the transcript. For details on RapMap (quasi-mapping in particular), please check out the associated paper. Note: RapMap implements both quasi- mapping and pseudo-alignment (originally introduced in Bray et al. 2016), these two are not the same thing. They are distinct concepts, and RapMap simply happens to implement algorithms for computing both.
There are three methods to install rapmap 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 rapmap Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install rapmap using apt-get by running the following command:
sudo apt-get -y install rapmap
Install rapmap Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install rapmap using apt by running the following command:
sudo apt -y install rapmap
Install rapmap 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 rapmap using aptitude by running the following command:
sudo aptitude -y install rapmap
How To Uninstall rapmap on Ubuntu 18.04
To uninstall only the rapmap package we can use the following command:
sudo apt-get remove rapmap
Uninstall rapmap And Its Dependencies
To uninstall rapmap and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove rapmap
Remove rapmap Configurations and Data
To remove rapmap configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge rapmap
Remove rapmap configuration, data, and all of its dependencies
We can use the following command to remove rapmap configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge rapmap
References
Summary
In this tutorial we learn how to install rapmap package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
