How To Install estwisedb 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 wise

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

What is estwisedb 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 estwisedb 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 estwisedb 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 estwisedb using apt by running the following command:

sudo apt -y install wise

Install estwisedb using apt

Because estwisedb 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 estwisedb using apt by running the following command:

sudo apt -y install wise

Install estwisedb 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 estwisedb by running the following command:

sudo aptitude -y install wise

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

sudo apt-get --only-upgrade install wise

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 wise

How To Uninstall estwisedb from Debian 11

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

sudo apt-get remove wise

Uninstall estwisedb and all its dependencies

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

sudo apt-get -y autoremove wise

Remove estwisedb with all configurations and data

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

sudo apt-get -y purge wise

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

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

sudo apt-get -y autoremove --purge wise

Extra info and code examples

Wise2 is a package focused on comparisons of biopolymers, commonly DNA and protein sequences. There are many other packages which do this, probably the best known being BLAST package (from NCBI) and the Fasta package (from Bill Pearson). There are other packages, such as the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused on hidden Markov models (HMMs) of biopolymers. Wise2's particular forte is the comparison of DNA sequence at the level of its protein translation. This comparison allows the simultaneous prediction of say gene structure with homology based alignment. Wise2 also contains other algorithms, such as the venerable Smith-Waterman algorithm, or more modern ones such as Stephen Altschul's generalised gap penalties, or even experimental ones developed in house, such as dba. The development of these algorithms is due to the ease of developing such algorithms in the environment used by Wise2. Wise2 has also been written with an eye for reuse and maintainability. Although it is a pure C package you can access its functionality directly in Perl. Parts of the package (or the entire package) can be used by other C or C++ programs without namespace clashes as all externally linked variables have the unique identifier Wise2 prepended.

Conclusion

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

See also: