How To Install roary on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 458 words
Introduction
In this tutorial we learn how to install roary on Ubuntu.
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 Ubuntu. 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 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 roary using aptitude by running the following command:
sudo aptitude -y install roary
How To Uninstall roary on Ubuntu
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 Ubuntu, we can use the command below:
sudo apt-get -y autoremove roary
Remove roary Configurations and Data
To remove roary configuration and data from Ubuntu 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
Summary
In this tutorial we learn how to install roary package on Ubuntu using different package management tools: apt, apt-get and aptitude.