How To Install transit-tpp on Kali Linux

In this guide, we’ll discuss How To Install transit-tpp on Kali Linux. Also, we will demonstrate how to uninstall and update transit-tpp.

One-liner install command

For those in a hurry, here's a one-line installation command:

sudo apt-get update && sudo apt -y install tnseq-transit

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

What is transit-tpp and what are the ways to install it?

Before beginning this tutorial, you will need access to a server or computer running Kali Linux. This guide was written specifically with a server running Kali Linux 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 Kali Linux. 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 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 transit-tpp using apt by running the following command:

sudo apt -y install tnseq-transit

Install transit-tpp using apt

Because transit-tpp is available in Kali Linux’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 transit-tpp using apt by running the following command:

sudo apt -y install tnseq-transit

Install transit-tpp 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 Kali Linux. Update apt database with aptitude using the following command.

sudo aptitude update

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

sudo aptitude -y install tnseq-transit

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

sudo apt-get --only-upgrade install tnseq-transit

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.

How To Uninstall transit-tpp from Kali Linux

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

sudo apt-get remove tnseq-transit

Uninstall transit-tpp and all its dependencies

To uninstall transit-tpp and its dependencies that are no longer needed by Kali Linux, you can use the command below:

sudo apt-get -y autoremove tnseq-transit

Remove transit-tpp with all configurations and data

To remove transit-tpp configuration and data from your system you can run the following purge command:

sudo apt-get -y purge tnseq-transit

Remove transit-tpp completely (configurations, data and all of its dependencies)

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

sudo apt-get -y autoremove --purge 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 apt, apt-get and aptitude tools. Also, we showed how to update as a single package and different ways to uninstall the transit-tpp from Kali Linux.

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 CentOS 8

How To Install transit-tpp on Ubuntu 22.04

How To Install transit-tpp on Ubuntu 21.04

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