How To Install python3-gfapy on Ubuntu 18.04
Introduction
In this tutorial we learn how to install python3-gfapy on Ubuntu 18.04.
What is python3-gfapy
python3-gfapy is:
The Graphical Fragment Assembly (GFA) are formats for the representation of sequence graphs, including assembly, variation and splicing graphs. Two versions of GFA have been defined (GFA1 and GFA2) and several sequence analysis programs have been adopting the formats as an interchange format, which allow the user to easily combine different sequence analysis tools.
This library implements the GFA1 and GFA2 specification. It is possible to create a Gfa object from a file in the GFA format or from scratch, to enumerate the graph elements (segments, links, containments, paths and header lines), to traverse the graph (by traversing all links outgoing from or incoming to a segment), to search for elements (e.g. which links connect two segments) and to manipulate the graph (e.g. to eliminate a link or a segment or to duplicate a segment distributing the read counts evenly on the copies).
The GFA format can be easily extended by users by defining own custom tags and record types. In Gfapy, it is easy to write extensions modules, which allow one to define custom record types and datatypes for the parsing and validation of custom fields. The custom lines can be connected, using references, to each other and to lines of the standard record types.
There are three methods to install python3-gfapy 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 python3-gfapy Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install python3-gfapy using apt-get by running the following command:
sudo apt-get -y install python3-gfapy
Install python3-gfapy Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install python3-gfapy using apt by running the following command:
sudo apt -y install python3-gfapy
Install python3-gfapy 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 python3-gfapy using aptitude by running the following command:
sudo aptitude -y install python3-gfapy
How To Uninstall python3-gfapy on Ubuntu 18.04
To uninstall only the python3-gfapy package we can use the following command:
sudo apt-get remove python3-gfapy
Uninstall python3-gfapy And Its Dependencies
To uninstall python3-gfapy and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove python3-gfapy
Remove python3-gfapy Configurations and Data
To remove python3-gfapy configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge python3-gfapy
Remove python3-gfapy configuration, data, and all of its dependencies
We can use the following command to remove python3-gfapy configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge python3-gfapy
References
Summary
In this tutorial we learn how to install python3-gfapy package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
