How To Install assign_taxonomy.py 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 qiime

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

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

sudo apt -y install qiime

Install assign_taxonomy.py using apt

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

sudo apt -y install qiime

Install assign_taxonomy.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 Ubuntu 22.04. Update apt database with aptitude using the following command.

sudo aptitude update

After updating aptitude database, You can install assign_taxonomy.py by running the following command:

sudo aptitude -y install qiime

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

sudo apt-get --only-upgrade install qiime

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 qiime

How To Uninstall assign_taxonomy.py from Ubuntu 22.04

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

sudo apt-get remove qiime

Uninstall assign_taxonomy.py and all its dependencies

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

sudo apt-get -y autoremove qiime

Remove assign_taxonomy.py with all configurations and data

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

sudo apt-get -y purge qiime

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

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

sudo apt-get -y autoremove --purge qiime

Extra info and code examples

QIIME (canonically pronounced ??Chime??) is a pipeline for performing microbial community analysis that integrates many third party tools which have become standard in the field. A standard QIIME analysis begins with sequence data from one or more sequencing platforms, including * Sanger, * Roche/454, and * Illumina GAIIx. With all the underlying tools installed, of which not all are yet available in Debian (or any other Linux distribution), QIIME can perform * library de-multiplexing and quality filtering; * denoising with PyroNoise; * OTU and representative set picking with uclust, cdhit, mothur, BLAST, or other tools; * taxonomy assignment with BLAST or the RDP classifier; * sequence alignment with PyNAST, muscle, infernal, or other tools; * phylogeny reconstruction with FastTree, raxml, clearcut, or other tools; * alpha diversity and rarefaction, including visualization of results, using over 20 metrics including Phylogenetic Diversity, chao1, and observed species; * beta diversity and rarefaction, including visualization of results, using over 25 metrics including weighted and unweighted UniFrac, Euclidean distance, and Bray-Curtis; * summarization and visualization of taxonomic composition of samples using pie charts and histograms and many other features. QIIME includes parallelization capabilities for many of the computationally intensive steps. By default, these are configured to utilize a mutli-core environment, and are easily configured to run in a cluster environment. QIIME is built in Python using the open-source PyCogent toolkit. It makes extensive use of unit tests, and is highly modular to facilitate custom analyses.

Conclusion

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

See also: