How To Install DASpatch 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 dascrubber

sudo dnf makecache && sudo dnf -y install dascrubber

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

What is DASpatch 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 DASpatch 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 DASpatch 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 DASpatch using dnf by running the following command:

sudo dnf -y install dascrubber

Install DASpatch on Fedora 34 using yum

Because DASpatch 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 DASpatch package on your server/computer by running the following command:

sudo yum -y install dascrubber

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

To update all the packages available on the system:

yum update

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

yum update dascrubber

To downgrade a package to an earlier version:

yum downgrade dascrubber

How to Upgrade DASpatch 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 dascrubber

How To remove DASpatch from Fedora 34

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

sudo dnf remove dascrubber

Extra info and code examples

The Dazzler Scrubbing Suite produces a set of edited reads that are guaranteed to * be continuous stretches of the underlying genome (i.e. no unremoved adapters and not chimers) * have no very low quality stretches (i.e. the error rate never exceeds some reasonable maximum, 20% or so in the case of Pacbio data). Its secondary goal is to do so with the minimum removal of data and splitting of reads.

Conclusion

You now have a full guide on how to install DASpatch using dnf and yum package managers. Also, we showed how to update manually as a single package and different ways to uninstall the DASpatch from Fedora 34.

See also: