How To Install transit-tpp on Fedora 34

In this tutorial, we will discuss How To Install transit-tpp on Fedora 34 using dnf and yum package managers. Also, we will demonstrate how to uninstall and update transit-tpp as well.

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 tnseq-transit
or if you use dnf:
sudo dnf makecache && sudo dnf -y install tnseq-transit

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

What is transit-tpp and How to Install It?

First things first, you will need access to a server or computer running Fedora 34. This guide was written specifically with a server running Fedora 34 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 transit-tpp on Fedora 34. 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 transit-tpp on Fedora 34 using dnf

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

sudo dnf makecache --refresh

After updating database, You can install transit-tpp using dnf by running the following command:

sudo dnf -y install tnseq-transit

Install transit-tpp on Fedora 34 using yum

Because transit-tpp is available in Fedora 34’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 transit-tpp package on your server/computer by running the following command:

sudo yum -y install tnseq-transit

How to upgrade (update) a single package transit-tpp using yum?

To update all the packages available on the system:

yum update

If you want to update a specific package like transit-tpp in this example you should use the following command:

yum update tnseq-transit

To downgrade a package to an earlier version:

yum downgrade tnseq-transit

How to Upgrade transit-tpp on Fedora 34 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 tnseq-transit

How To remove transit-tpp from Fedora 34

To uninstall only the transit-tpp package you can execute the following command:

sudo dnf remove tnseq-transit

Extra info and code examples

This is a software that can be used to analyze Tn-Seq datasets. It includes various statistical calculations of essentiality of genes or genomic regions (including conditional essentiality between 2 conditions). These methods were developed and tested as a collaboration between the Sassetti lab (UMass) and the Ioerger lab (Texas A&M) TRANSIT is capable of analyzing TnSeq libraries constructed with Himar1 or Tn5 datasets. TRANSIT assumes you have already done pre-processing of raw sequencing files (.fastq) and extracted read counts into a .wig formatted file. The .wig file should contain the counts at all sites where an insertion could take place (including sites with no reads). For Himar1 datasets this is all TA sites in the genome. For Tn5 datasets this would be all nucleotides in the genome.

Conclusion

You now have a full guide on how to install transit-tpp using dnf and yum package managers. Also, we showed how to update manually as a single package and different ways to uninstall the transit-tpp from Fedora 34.

See also:

How To Install transit-tpp on Kali Linux

How To Install transit-tpp on Debian 11

How To Install transit-tpp on Fedora 34

How To Install transit-tpp on Ubuntu 22.04

How To Install transit-tpp on Ubuntu 21.04

How To Install transit-tpp on CentOS 8

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