How To Install assign_taxonomy.py on CentOS 8

One-liner Install Command

If you are only interested in the installation command, here is a quick answer for you:

sudo yum makecache && sudo yum -y install qiime

sudo dnf makecache && sudo dnf -y install qiime

But if you are interested in the details with step-by-step instructions, the following information will be helpful.

What is assign_taxonomy.py and How to Install It?

First things first, you will need access to a server or computer running CentOS 8. This guide was written specifically with a server running CentOS 8 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 CentOS 8. 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 on CentOS 8 using dnf

First, update dnf packages database with dnf by running the next command:

sudo dnf makecache --refresh

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

sudo dnf -y install qiime

Install assign_taxonomy.py on CentOS 8 using yum

Because assign_taxonomy.py is available in CentOS 8’s default repositories, it is possible to install it from these repositories using the yum packaging system.

To begin, update local packages database with yum using the following command.

sudo yum makecache --refresh

Now can install assign_taxonomy.py package on your server/computer by running the following command:

sudo yum -y install qiime

How to upgrade (update) a single package assign_taxonomy.py using yum?

To update all the packages available on the system:

yum update

If you want to update a specific package like assign_taxonomy.py in this example you should use the following command:

yum update qiime

To downgrade a package to an earlier version:

yum downgrade qiime

How to Upgrade assign_taxonomy.py on CentOS 8 with dnf?

When you run the dnf update, all system packages with available updates are updated. However, if you want to upgrade a single package, then you would have to pass the package name as the argument to the dnf update command.

dnf update qiime

How To remove assign_taxonomy.py from CentOS 8

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

sudo dnf remove 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 dnf and yum package managers. Also, we showed how to update manually as a single package and different ways to uninstall the assign_taxonomy.py from CentOS 8.

See also: