How To Install jalview on Debian 11
Introduction
In this tutorial we learn how to install jalview on Debian 11.
What is jalview
jalview is:
JalView is a Java DNA, RNA and protein sequence alignment editor that can work with sequence alignments produced by programs implementing alignment algorithms such as clustalw, kalign and t-coffee.
It has lots of features, is actively developed, and will compare advantageously to BioEdit, while being free as in free speech!
There are three methods to install jalview on Debian 11. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install jalview Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install jalview using apt-get by running the following command:
sudo apt-get -y install jalview
Install jalview Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install jalview using apt by running the following command:
sudo apt -y install jalview
Install jalview 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 jalview using aptitude by running the following command:
sudo aptitude -y install jalview
How To Uninstall jalview on Debian 11
To uninstall only the jalview package we can use the following command:
sudo apt-get remove jalview
Uninstall jalview And Its Dependencies
To uninstall jalview and its dependencies that are no longer needed by Debian 11, we can use the command below:
sudo apt-get -y autoremove jalview
Remove jalview Configurations and Data
To remove jalview configuration and data from Debian 11 we can use the following command:
sudo apt-get -y purge jalview
Remove jalview configuration, data, and all of its dependencies
We can use the following command to remove jalview configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge jalview
Dependencies
jalview have the following dependencies:
- default-jre
- debconf
- libcommons-discovery-java
- libjaxws-java
- groovy
- javahelp2
- libapache-mime4j-java
- libaxis-java
- libbiojava4.0-java
- libhtsjdk-java
- libhttpclient-java
- libhttpcore-java
- libhttpmime-java
- libintervalstorej-java
- libjaba-client-java
- libjaxrs-api-java
- libjersey1-client-java
- libjersey1-core-java
- libjetty9-java
- libjfreesvg-java
- libjmol-java
- libjson-simple-java
- libjsoup-java
- libjswingreader-java
- liblog4j1.2-java
- libmiglayout-java
- libslf4j-java
- libvamsas-client-java
- varna
- debconf
References
Summary
In this tutorial we learn how to install jalview package on Debian 11 using different package management tools: apt, apt-get and aptitude.