How To Install assign_taxonomy.py on CentOS 8
In this tutorial, we will discuss How To Install assign_taxonomy.py on CentOS 8
yum package managers.
Also, we will demonstrate how to uninstall and update
assign_taxonomy.py as well.
If you are only interested in the installation command, here is a quick answer for you:
or if you use
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.
Short description: Quantitative Insights Into Microbial Ecology
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.
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
sudo dnf -y install qiime
Because assign_taxonomy.py is available in CentOS 8’s default
it is possible to install it from these repositories using the
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
To update all the packages available on the system:
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
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
To uninstall only the
assign_taxonomy.py package you can execute
sudo dnf remove qiime
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.
- Maintainer: unknown
- Sources url: unknown
- Section/Category: unknown
You now have a full guide on how to install
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.