How To Install bcbio on Debian 12
Introduction
In this tutorial we learn how to install bcbio on Debian 12.
What is bcbio
bcbio is:
This package installs the command line tools of the bcbio-nextgen toolkit implementing best-practice pipelines for fully automated high throughput sequencing analysis.
A high-level configuration file specifies inputs and analysis parameters to drive a parallel pipeline that handles distributed execution, idempotent processing restarts and safe transactional steps. The project contributes a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology.
This package builds and having it in Debian unstable helps the Debian developers to synchronize their efforts. But unless a series of external dependencies are not installed manually, the functionality of bcbio in Debian is only a shadow of itself. Please use the official distribution of bcbio for the time being, which means “use conda”. The TODO file in the Debian directory should give an overview on progress for Debian packaging.
There are three methods to install bcbio 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 bcbio Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install bcbio using apt-get by running the following command:
sudo apt-get -y install bcbio
Install bcbio Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install bcbio using apt by running the following command:
sudo apt -y install bcbio
Install bcbio 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 bcbio using aptitude by running the following command:
sudo aptitude -y install bcbio
How To Uninstall bcbio on Debian 12
To uninstall only the bcbio package we can use the following command:
sudo apt-get remove bcbio
Uninstall bcbio And Its Dependencies
To uninstall bcbio and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove bcbio
Remove bcbio Configurations and Data
To remove bcbio configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge bcbio
Remove bcbio configuration, data, and all of its dependencies
We can use the following command to remove bcbio configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge bcbio
Dependencies
bcbio have the following dependencies:
References
Summary
In this tutorial we learn how to install bcbio package on Debian 12 using different package management tools: apt, apt-get and aptitude.