How To Install tnseq-transit on Ubuntu 18.04
Introduction
In this tutorial we learn how to install tnseq-transit on Ubuntu 18.04.
What is tnseq-transit
tnseq-transit is:
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.
There are three methods to install tnseq-transit on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install tnseq-transit Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install tnseq-transit using apt-get by running the following command:
sudo apt-get -y install tnseq-transit
Install tnseq-transit Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install tnseq-transit using apt by running the following command:
sudo apt -y install tnseq-transit
Install tnseq-transit 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. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install tnseq-transit using aptitude by running the following command:
sudo aptitude -y install tnseq-transit
How To Uninstall tnseq-transit on Ubuntu 18.04
To uninstall only the tnseq-transit package we can use the following command:
sudo apt-get remove tnseq-transit
Uninstall tnseq-transit And Its Dependencies
To uninstall tnseq-transit and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove tnseq-transit
Remove tnseq-transit Configurations and Data
To remove tnseq-transit configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge tnseq-transit
Remove tnseq-transit configuration, data, and all of its dependencies
We can use the following command to remove tnseq-transit configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge tnseq-transit
References
Summary
In this tutorial we learn how to install tnseq-transit package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
