How To Install bash5tools.py 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 pbh5tools

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

What is bash5tools.py 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 bash5tools.py 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 bash5tools.py 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 bash5tools.py using apt by running the following command:

sudo apt -y install pbh5tools

Install bash5tools.py using apt

Because bash5tools.py 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 bash5tools.py using apt by running the following command:

sudo apt -y install pbh5tools

Install bash5tools.py 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 bash5tools.py by running the following command:

sudo aptitude -y install pbh5tools

How to upgrade (update) a single package bash5tools.py 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 bash5tools.py, e.g. single package, you should use the following format with the apt-get command/apt command:

sudo apt-get --only-upgrade install pbh5tools

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 pbh5tools

How To Uninstall bash5tools.py from Debian 11

To uninstall only the bash5tools.py package you can execute the following command:

sudo apt-get remove pbh5tools

Uninstall bash5tools.py and all its dependencies

To uninstall bash5tools.py and its dependencies that are no longer needed by Debian 11, you can use the command below:

sudo apt-get -y autoremove pbh5tools

Remove bash5tools.py with all configurations and data

To remove bash5tools.py configuration and data from your system you can run the following purge command:

sudo apt-get -y purge pbh5tools

Remove bash5tools.py completely (configurations, data and all of its dependencies)

And lastly, you can run the next command to remove absolutely everything related to bash5tools.py package, e.g.: configurations, data and all of its dependencies. Just use this command:

sudo apt-get -y autoremove --purge pbh5tools

Extra info and code examples

This package provides functionality for manipulating and extracting data from cmp.h5 and bas.h5 files produced by the Pacific Biosciences sequencers. cmp.h5 files contain alignment information while bas.h5 files contain base-call information. This package is part of the SMRTAnalysis suite.

Conclusion

You now have a full guide on how to install bash5tools.py using apt, apt-get and aptitude tools. Also, we showed how to update as a single package and different ways to uninstall the bash5tools.py from Debian 11.

See also: