How To Install python-ngs on Ubuntu 18.04
Introduction
In this tutorial we learn how to install python-ngs on Ubuntu 18.04.
What is python-ngs
python-ngs is:
NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously. It also provides a library for building new back-end “engines”. The engine for accessing SRA data is contained within the sister repository ncbi-vdb.
The API is currently expressed in C++, Java and Python languages. The design makes it possible to maintain a high degree of similarity between the code in one language and code in another - especially between C++ and Java.
Python bindings.
There are three methods to install python-ngs on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install python-ngs Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install python-ngs using apt-get by running the following command:
sudo apt-get -y install python-ngs
Install python-ngs Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install python-ngs using apt by running the following command:
sudo apt -y install python-ngs
Install python-ngs 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 python-ngs using aptitude by running the following command:
sudo aptitude -y install python-ngs
How To Uninstall python-ngs on Ubuntu 18.04
To uninstall only the python-ngs package we can use the following command:
sudo apt-get remove python-ngs
Uninstall python-ngs And Its Dependencies
To uninstall python-ngs and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove python-ngs
Remove python-ngs Configurations and Data
To remove python-ngs configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge python-ngs
Remove python-ngs configuration, data, and all of its dependencies
We can use the following command to remove python-ngs configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge python-ngs
References
Summary
In this tutorial we learn how to install python-ngs package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
