How To Install python3-slow5 on Debian 12
Introduction
In this tutorial we learn how to install python3-slow5 on Debian 12.
What is python3-slow5
python3-slow5 is:
Slow5lib is a software library for reading & writing SLOW5 files. Slow5lib is designed to facilitate use of data in SLOW5 format by third- party software packages. Existing packages that read/write data in FAST5 format can be easily modified to support SLOW5.
SLOW5 is a new file format for storing signal data from Oxford Nanopore Technologies (ONT) devices. SLOW5 was developed to overcome inherent limitations in the standard FAST5 signal data format that prevent efficient, scalable analysis and cause many headaches for developers. SLOW5 can be encoded in human-readable ASCII format, or a more compact and efficient binary format (BLOW5) - this is analogous to the seminal SAM/BAM format for storing DNA sequence alignments. The BLOW5 binary format supports zlib (DEFLATE) compression, or other compression methods, thereby minimising the data storage footprint while still permitting efficient parallel access. Detailed benchmarking experiments have shown that SLOW5 format is an order of magnitude faster and significantly smaller than FAST5.
This is the Python3 module.
There are three methods to install python3-slow5 on Debian 12. 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-slow5 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-slow5 using apt-get by running the following command:
sudo apt-get -y install python3-slow5
Install python3-slow5 Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install python3-slow5 using apt by running the following command:
sudo apt -y install python3-slow5
Install python3-slow5 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 python3-slow5 using aptitude by running the following command:
sudo aptitude -y install python3-slow5
How To Uninstall python3-slow5 on Debian 12
To uninstall only the python3-slow5 package we can use the following command:
sudo apt-get remove python3-slow5
Uninstall python3-slow5 And Its Dependencies
To uninstall python3-slow5 and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove python3-slow5
Remove python3-slow5 Configurations and Data
To remove python3-slow5 configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge python3-slow5
Remove python3-slow5 configuration, data, and all of its dependencies
We can use the following command to remove python3-slow5 configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge python3-slow5
Dependencies
python3-slow5 have the following dependencies:
References
Summary
In this tutorial we learn how to install python3-slow5 package on Debian 12 using different package management tools: apt, apt-get and aptitude.