How To Install roary on Kali Linux

Introduction

In this tutorial we learn how to install roary on Kali Linux.

What is roary

roary is:

Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (as produced, for instance, by Prokka) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and hundreds of GB of RAM. Roary is not intended for meta-genomics or for comparing extremely diverse sets of genomes.

There are three methods to install roary on Kali Linux. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install roary Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install roary using apt-get by running the following command:

sudo apt-get -y install roary

Install roary Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install roary using apt by running the following command:

sudo apt -y install roary

Install roary Using aptitude

If you want to follow this method, you might need to install aptitude on Kali Linux 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 apt database, We can install roary using aptitude by running the following command:

sudo aptitude -y install roary

How To Uninstall roary on Kali Linux

To uninstall only the roary package we can use the following command:

sudo apt-get remove roary

Uninstall roary And Its Dependencies

To uninstall roary and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove roary

Remove roary Configurations and Data

To remove roary configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge roary

Remove roary configuration, data, and all of its dependencies

We can use the following command to remove roary configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge roary

Dependencies

roary have the following dependencies:

• perl
• bioperl
• libarray-utils-perl
• libdigest-md5-file-perl
• libenv-path-perl
• libexception-class-perl
• libfile-find-rule-perl
• libfile-grep-perl
• libfile-slurper-perl
• libfile-which-perl
• libfindbin-libs-perl
• libgraph-perl
• libgraph-readwrite-perl
• liblog-log4perl-perl
• libmoose-perl
• libperlio-utf8-strict-perl
• libtest-most-perl
• libtest-file-perl
• libtest-files-perl
• libtest-output-perl
• libtext-csv-perl
• bedtools
• cd-hit
• ncbi-blast+
• mcl
• parallel
• prank
• r-base-core
• r-cran-ggplot2
• mafft
• fasttree

References

• roary website

Summary

In this tutorial we learn how to install roary package on Kali Linux using different package management tools: apt, apt-get and aptitude.