How To Install gbrowse on Debian 10
Introduction
In this tutorial we learn how to install gbrowse on Debian 10.
What is gbrowse
gbrowse is:
Generic Genome Browser is a simple but highly configurable web-based genome browser. It is a component of the Generic Model Organism Systems Database project (GMOD). Some of its features:
- Simultaneous bird’s eye and detailed views of the genome;
- Scroll, zoom, center;
- Attach arbitrary URLs to any annotation;
- Order and appearance of tracks are customizable by administrator and end-user;
- Search by annotation ID, name, or comment;
- Supports third party annotation using GFF formats;
- Settings persist across sessions;
- DNA and GFF dumps;
- Connectivity to different databases, including BioSQL and Chado;
- Multi-language support;
- Third-party feature loading;
- Customizable plug-in architecture (e.g. run BLAST, dump & import many formats, find oligonucleotides, design primers, create restriction maps, edit features).
There are three methods to install gbrowse on Debian 10. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install gbrowse Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install gbrowse using apt-get by running the following command:
sudo apt-get -y install gbrowse
Install gbrowse Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install gbrowse using apt by running the following command:
sudo apt -y install gbrowse
Install gbrowse 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 Debian. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install gbrowse using aptitude by running the following command:
sudo aptitude -y install gbrowse
How To Uninstall gbrowse on Debian 10
To uninstall only the gbrowse package we can use the following command:
sudo apt-get remove gbrowse
Uninstall gbrowse And Its Dependencies
To uninstall gbrowse and its dependencies that are no longer needed by Debian 10, we can use the command below:
sudo apt-get -y autoremove gbrowse
Remove gbrowse Configurations and Data
To remove gbrowse configuration and data from Debian 10 we can use the following command:
sudo apt-get -y purge gbrowse
Remove gbrowse configuration, data, and all of its dependencies
We can use the following command to remove gbrowse configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge gbrowse
Dependencies
gbrowse have the following dependencies:
- perl
- apache2
- bioperl
- libbio-graphics-perl
- libbio-coordinate-perl
- libcgi-session-perl
- libgd-gd2-noxpm-perl
- libio-string-perl
- libjson-perl
- libstatistics-descriptive-perl
- libwww-perl
- libhttp-daemon-perl
- libterm-readkey-perl
- sqlite3
- libdbd-sqlite3-perl
- libjs-prototype
- libjs-scriptaculous
- libvm-ec2-perl
- lsb-base
References
Summary
In this tutorial we learn how to install gbrowse package on Debian 10 using different package management tools: apt, apt-get and aptitude.
