How To Install sra_to_solid on Ubuntu 22.04

One-liner install command

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

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

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

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

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 sra_to_solid 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 sra_to_solid 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 sra_to_solid using apt by running the following command:

sudo apt -y install tophat

Install sra_to_solid using apt

Because sra_to_solid 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 sra_to_solid using apt by running the following command:

sudo apt -y install tophat

Install sra_to_solid 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 sra_to_solid by running the following command:

sudo aptitude -y install tophat

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

sudo apt-get --only-upgrade install tophat

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 tophat

How To Uninstall sra_to_solid from Ubuntu 22.04

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

sudo apt-get remove tophat

Uninstall sra_to_solid and all its dependencies

To uninstall sra_to_solid and its dependencies that are no longer needed by Ubuntu 22.04, you can use the command below:

sudo apt-get -y autoremove tophat

Remove sra_to_solid with all configurations and data

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

sudo apt-get -y purge tophat

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

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

sudo apt-get -y autoremove --purge tophat

Extra info and code examples

TopHat aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. TopHat is a collaborative effort between the University of Maryland Center for Bioinformatics and Computational Biology and the University of California, Berkeley Departments of Mathematics and Molecular and Cell Biology.

Conclusion

You now have a full guide on how to install sra_to_solid using apt, apt-get and aptitude tools. Also, we showed how to update as a single package and different ways to uninstall the sra_to_solid from Ubuntu 22.04.

See also: