How To Install stops 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 staden

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

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

sudo apt -y install staden

Install stops using apt

Because stops 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 stops using apt by running the following command:

sudo apt -y install staden

Install stops 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 stops by running the following command:

sudo aptitude -y install staden

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

sudo apt-get --only-upgrade install staden

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 staden

How To Uninstall stops from Debian 11

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

sudo apt-get remove staden

Uninstall stops and all its dependencies

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

sudo apt-get -y autoremove staden

Remove stops with all configurations and data

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

sudo apt-get -y purge staden

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

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

sudo apt-get -y autoremove --purge staden

Extra info and code examples

Staden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin). Gap4 performs sequence assembly, contig ordering based on read pair data, contig joining based on sequence comparisons, assembly checking, repeat searching, experiment suggestion, read pair analysis and contig editing. It has graphical views of contigs, templates, readings and traces which all scroll in register. Contig editor searches and experiment suggestion routines use confidence values to calculate the confidence of the consensus sequence and hence identify only places requiring visual trace inspection or extra data. The result is extremely rapid finishing and a consensus of known accuracy. Pregap4 provides a graphical user interface to set up the processing required to prepare trace data for assembly or analysis, and automates these processes. Trev is a rapid and flexible viewer and editor for ABI, ALF, SCF and ZTR trace files. Prefinish analyses partially completed sequence assemblies and suggests the most efficient set of experiments to help finish the project. Tracediff and hetscan automatically locate mutations by comparing trace data against reference traces. They annotate the mutations found ready for viewing in gap4. Spin analyses nucleotide sequences to find genes, restriction sites, motifs, etc. It can perform translations, find open reading frames, count codons, etc. Many results are presented graphically and a sliding sequence window is linked to the graphics cursor. Spin also compares pairs of sequences in many ways. It has very rapid dot matrix analysis, global and local alignment algorithms, plus a sliding sequence window linked to the graphical plots. It can compare nucleic acid against nucleic acid, protein against protein, and protein against nucleic acid.

Conclusion

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

See also: