How To Install rapmap on Debian 9

In this tutorial we learn how to install rapmap on Debian 9. rapmap is rapid sensitive and accurate DNA read mapping via quasi-mapping

Introduction

In this tutorial we learn how to install rapmap on Debian 9.

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 Debian 9. 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 Debian. 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 Debian 9

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 Debian 9, we can use the command below:

sudo apt-get -y autoremove rapmap

Remove rapmap Configurations and Data

To remove rapmap configuration and data from Debian 9 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

Dependencies

rapmap have the following dependencies:

References

Summary

In this tutorial we learn how to install rapmap package on Debian 9 using different package management tools: apt, apt-get and aptitude.