How To Install slclust on Debian 11

One-liner install command

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

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

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

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

Before beginning this tutorial, you will need access to a server or computer running Debian 11. This guide was written specifically with a server running Debian 11 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 slclust on Debian 11. 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 slclust 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 slclust using apt by running the following command:

sudo apt -y install trinityrnaseq

Install slclust using apt

Because slclust is available in Debian 11’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 slclust using apt by running the following command:

sudo apt -y install trinityrnaseq

Install slclust 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 11. Update apt database with aptitude using the following command.

sudo aptitude update

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

sudo aptitude -y install trinityrnaseq

How to upgrade (update) a single package slclust 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 slclust, e.g. single package, you should use the following format with the apt-get command/apt command:

sudo apt-get --only-upgrade install trinityrnaseq

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 trinityrnaseq

How To Uninstall slclust from Debian 11

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

sudo apt-get remove trinityrnaseq

Uninstall slclust and all its dependencies

To uninstall slclust and its dependencies that are no longer needed by Debian 11, you can use the command below:

sudo apt-get -y autoremove trinityrnaseq

Remove slclust with all configurations and data

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

sudo apt-get -y purge trinityrnaseq

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

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

sudo apt-get -y autoremove --purge trinityrnaseq

Extra info and code examples

Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.

Conclusion

You now have a full guide on how to install slclust using apt, apt-get and aptitude tools. Also, we showed how to update as a single package and different ways to uninstall the slclust from Debian 11.

See also: