How To Install run_mapsembler2_pipeline on Kali Linux

One-liner install command

For those in a hurry, here's a one-line installation command:

sudo apt-get update && sudo apt -y install mapsembler2

But if you are interested in the detailed steps with descriptions, the following information is for you.

What is run_mapsembler2_pipeline and what are the ways to install it?

Before beginning this tutorial, you will need access to a server or computer running Kali Linux. This guide was written specifically with a server running Kali Linux in mind, although it should also work on older, supported versions of the operating system.

Also, make sure you are running a regular, non-root user with sudo privileges configured on your server. When you have an account available, log in as your non-root user to begin.

There are several ways to install run_mapsembler2_pipeline on Kali Linux. You can use (links are clickable):

In the following sections, we will describe each method in detail. You can choose one of them or refer to the recommended one.

Install run_mapsembler2_pipeline using apt-get

First, update apt database with apt-get using the following command.

sudo apt-get update

After updating apt-get database, You can install run_mapsembler2_pipeline using apt by running the following command:

sudo apt -y install mapsembler2

Install run_mapsembler2_pipeline using apt

Because run_mapsembler2_pipeline is available in Kali Linux’s default repositories, it is possible to install it from these repositories using the apt packaging system.

To begin, update apt database with apt using the following command.

sudo apt update

After updating apt database, You can install run_mapsembler2_pipeline using apt by running the following command:

sudo apt -y install mapsembler2

Install run_mapsembler2_pipeline 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 Kali Linux. Update apt database with aptitude using the following command.

sudo aptitude update

After updating aptitude database, You can install run_mapsembler2_pipeline by running the following command:

sudo aptitude -y install mapsembler2

How to upgrade (update) a single package run_mapsembler2_pipeline using apt-get?

First, you will need to update packages index. Run update command as usual:

sudo apt-get update

Next, to upgrade only the run_mapsembler2_pipeline, e.g. single package, you should use the following format with the apt-get command/apt command:

sudo apt-get --only-upgrade install mapsembler2

Note that this command will not install any new packages! If you wish to install the package if it doesn't exist you may leave out --only-upgrade part.

sudo apt-get install mapsembler2

How To Uninstall run_mapsembler2_pipeline from Kali Linux

To uninstall only the run_mapsembler2_pipeline package you can execute the following command:

sudo apt-get remove mapsembler2

Uninstall run_mapsembler2_pipeline and all its dependencies

To uninstall run_mapsembler2_pipeline and its dependencies that are no longer needed by Kali Linux, you can use the command below:

sudo apt-get -y autoremove mapsembler2

Remove run_mapsembler2_pipeline with all configurations and data

To remove run_mapsembler2_pipeline configuration and data from your system you can run the following purge command:

sudo apt-get -y purge mapsembler2

Remove run_mapsembler2_pipeline completely (configurations, data and all of its dependencies)

And lastly, you can run the next command to remove absolutely everything related to run_mapsembler2_pipeline package, e.g.: configurations, data and all of its dependencies. Just use this command:

sudo apt-get -y autoremove --purge mapsembler2

Extra info and code examples

Mapsembler2 is a targeted assembly software. It takes as input a set of NGS raw reads (fasta or fastq, gzipped or not) and a set of input sequences (starters). It first determines if each starter is read-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then for each read-coherent starter, Mapsembler2 outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice. Mapsembler2 may be used for (not limited to): - Validate an assembled sequence (input as starter), e.g. from a de Bruijn graph assembly where read-coherence was not enforced. - Checks if a gene (input as starter) has an homolog in a set of reads - Checks if a known enzyme is present in a metagenomic NGS read set. - Enrich unmappable reads by extending them, possibly making them mappable - Checks what happens at the extremities of a contig - Remove contaminants or symbiont reads from a read set

Conclusion

You now have a full guide on how to install run_mapsembler2_pipeline using apt, apt-get and aptitude tools. Also, we showed how to update as a single package and different ways to uninstall the run_mapsembler2_pipeline from Kali Linux.

See also: