How To Install run_mapsembler2_pipeline on Fedora 34

One-liner Install Command

If you are only interested in the installation command, here is a quick answer for you:

sudo yum makecache && sudo yum -y install mapsembler2

sudo dnf makecache && sudo dnf -y install mapsembler2

But if you are interested in the details with step-by-step instructions, the following information will be helpful.

What is run_mapsembler2_pipeline and How to Install It?

First things first, you will need access to a server or computer running Fedora 34. This guide was written specifically with a server running Fedora 34 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 Fedora 34. 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 on Fedora 34 using dnf

First, update dnf packages database with dnf by running the next command:

sudo dnf makecache --refresh

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

sudo dnf -y install mapsembler2

Install run_mapsembler2_pipeline on Fedora 34 using yum

Because run_mapsembler2_pipeline is available in Fedora 34’s default repositories, it is possible to install it from these repositories using the yum packaging system.

To begin, update local packages database with yum using the following command.

sudo yum makecache --refresh

Now can install run_mapsembler2_pipeline package on your server/computer by running the following command:

sudo yum -y install mapsembler2

How to upgrade (update) a single package run_mapsembler2_pipeline using yum?

To update all the packages available on the system:

yum update

If you want to update a specific package like run_mapsembler2_pipeline in this example you should use the following command:

yum update mapsembler2

To downgrade a package to an earlier version:

yum downgrade mapsembler2

How to Upgrade run_mapsembler2_pipeline on Fedora 34 with dnf?

When you run the dnf update, all system packages with available updates are updated. However, if you want to upgrade a single package, then you would have to pass the package name as the argument to the dnf update command.

dnf update mapsembler2

How To remove run_mapsembler2_pipeline from Fedora 34

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

sudo dnf remove 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 dnf and yum package managers. Also, we showed how to update manually as a single package and different ways to uninstall the run_mapsembler2_pipeline from Fedora 34.

See also: