How To Install cgview on Ubuntu

Posted on April 1, 2023 (Last modified on May 20, 2023 )

4 minutes • 704 words

Introduction

In this tutorial we learn how to install cgview on Ubuntu.

What is `cgview`

cgview is:

CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web. Feature information and rendering options are supplied to the program using an XML file, a tab delimited file, or an NCBI ptt file. CGView converts the input into a graphical map (PNG, JPG, or Scalable Vector Graphics format), complete with labels, a title, legends, and footnotes. In addition to the default full view map, the program can generate a series of hyperlinked maps showing expanded views. The linked maps can be explored using any web browser, allowing rapid genome browsing, and facilitating data sharing. The feature labels in maps can be hyperlinked to external resources, allowing CGView maps to be integrated with existing web site content or databases.

In addition to the CGView application, an API is available for generating maps from within other Java applications, using the cgview package.

CGView can be used for any of the following:

Bacterial genome visualization and browsing - CGView can be incorporated into bacterial genome annotation pipelines, as a means of generating web content for data visualization and navigation. The PNG and image map content does not require Java applets or special browser plugins.
Genome poster generation - CGView can generate poster-sized images of circular genomes in rasterized image formats or in Scalable Vector Graphics format.
Sequence analysis visualization - CGView can be used to display the output of sequence analysis programs in a circular context.

CGView features:

Images can be generated in PNG, JPG, or SVG format. See the CGView gallery.
Static or interactive maps can be generated. The interactive maps make use of standard PNG images and HTML image maps. Scalable Vector Graphics output is included in the interactive maps (see example).
The XML input allows complete control over the appearance of the map.
Tab delimited input files and NCBI ptt files can be used as an alternative to the XML format.
The CGView API can be used to incorporate CGView into Java applications.
The CGView applet can be used to incorporate zoomable maps into web pages (see example).
The CGView Server can be used to generate maps online.

There are three methods to install cgview 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 cgview Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install cgview

Install cgview Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install cgview

Install cgview 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 cgview using aptitude by running the following command:

sudo aptitude -y install cgview

How To Uninstall cgview on Ubuntu

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

sudo apt-get remove cgview

Uninstall cgview And Its Dependencies

To uninstall cgview and its dependencies that are no longer needed by Ubuntu, we can use the command below:

sudo apt-get -y autoremove cgview

Remove cgview Configurations and Data

To remove cgview configuration and data from Ubuntu we can use the following command:

sudo apt-get -y purge cgview

Remove cgview configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge cgview

Dependencies

cgview have the following dependencies:

References

cgview website

Summary

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