cgview command not found

In this troubleshooting guide we learn how to fix cgview command not found error message

Introduction

When you run more command in linux terminal / console, you get the following error message

cgview: command not found

or when using sudo you get the following error message

sudo: cgview: command not found

Solutions to cgview: command not found

How To Fix cgview: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu cgview is provided by cgview package.

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.

To fix this problem, we can install more using the command below.

sudo apt-get -y install cgview

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install cgview.

sudo apt -y install cgview

Or if you have aptitude installed you can use the following command.

sudo aptitude install cgview

Summary

In this tutorial we learn how to fix cgview command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.