How To Install ssw_test on Ubuntu 22.04
In this guide, we’ll discuss How To Install ssw_test on Ubuntu 22.04.
Also, we will demonstrate how to uninstall and update
ssw_test
.
One-liner install command
For those in a hurry, here's a one-line installation command:
sudo apt-get update && sudo apt -y install ssw-align
But if you are interested in the detailed steps with descriptions, the following information is for you.
What is ssw_test
and what are
the ways to install it?
Short description: Smith-Waterman aligner based on libssw
Before beginning this tutorial, you will need access to a server or computer running Ubuntu 22.04. This guide was written specifically with a server running Ubuntu 22.04 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 ssw_test on Ubuntu 22.04. 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 ssw_test 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 ssw_test using apt
by running the
following command:
sudo apt -y install ssw-align
Install ssw_test using apt
Because ssw_test is available in Ubuntu 22.04’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 ssw_test using apt
by running the
following command:
sudo apt -y install ssw-align
Install ssw_test 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 Ubuntu 22.04. Update apt database with aptitude using the following command.
sudo aptitude update
After updating aptitude
database,
You can install ssw_test by running the following command:
sudo aptitude -y install ssw-align
How to upgrade (update) a single package ssw_test 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 ssw_test, e.g. single package, you should use the following format with the apt-get command/apt command:
sudo apt-get --only-upgrade install ssw-align
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.
It's Good to Know:
sudo apt-get install ssw-align
This will upgrade the package even if is already installed.
How To Uninstall ssw_test from Ubuntu 22.04
To uninstall only the ssw_test
package you can execute
the
following command:
sudo apt-get remove ssw-align
Uninstall ssw_test and all its dependencies
To uninstall ssw_test and its dependencies that are no longer needed by Ubuntu 22.04, you can use the command below:
sudo apt-get -y autoremove ssw-align
Remove ssw_test with all configurations and data
To remove ssw_test configuration and data
from your system you can run the following purge
command:
sudo apt-get -y purge ssw-align
Remove ssw_test completely (configurations, data and all of its dependencies)
And lastly, you can run the next command to remove absolutely everything related to ssw_test package, e.g.: configurations, data and all of its dependencies. Just use this command:
sudo apt-get -y autoremove --purge ssw-align
Extra info and code examples
This package provides a command-line aligner based on the libssw library, a fast SIMD accelerated implementation of the Smith-Waterman algorithm. The input files can be in FASTA or FASTQ format. Both target and query files can contain multiple sequences. Each sequence in the query file will be aligned with all sequences in the target file. Output is provided in SAM or BLAST-like text format.
- Maintainer: Debian Med Packaging Team
- Sources url: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library
- Section/Category: science
Conclusion
You now have a full guide on how to install ssw_test
using apt, apt-get and aptitude tools.
Also, we showed how to update as a single package and different ways to uninstall
the ssw_test from Ubuntu 22.04.