How To Install stacks-setup-database 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 stacks-web

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

What is stacks-setup-database 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 stacks-setup-database 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 stacks-setup-database 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 stacks-setup-database using apt by running the following command:

sudo apt -y install stacks-web

Install stacks-setup-database using apt

Because stacks-setup-database 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 stacks-setup-database using apt by running the following command:

sudo apt -y install stacks-web

Install stacks-setup-database 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 stacks-setup-database by running the following command:

sudo aptitude -y install stacks-web

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

sudo apt-get --only-upgrade install stacks-web

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 stacks-web

How To Uninstall stacks-setup-database from Debian 11

To uninstall only the stacks-setup-database package you can execute the following command:

sudo apt-get remove stacks-web

Uninstall stacks-setup-database and all its dependencies

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

sudo apt-get -y autoremove stacks-web

Remove stacks-setup-database with all configurations and data

To remove stacks-setup-database configuration and data from your system you can run the following purge command:

sudo apt-get -y purge stacks-web

Remove stacks-setup-database completely (configurations, data and all of its dependencies)

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

sudo apt-get -y autoremove --purge stacks-web

Extra info and code examples

Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. This package provides the web-based viewer which you can use to examine Stacks output that has been loaded into a MySQL database.

Conclusion

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

See also: