How To Install smalr on Debian 10
Introduction
In this tutorial we learn how to install smalr on Debian 10.
What is smalr
smalr is:
The SMALR package conducts single-molecule level interrogation of the methylation status of single-molecule real-time (SMRT) sequencing reads. There are two protocols available for use within the pipeline, SMsn and SMp.
- SMsn: Single-molecule, single nucleotide analysis Each motif site on each sequencing molecule is assessed for methylation status. This is designed for use with short (~250bp) sequencing library preps, where the long read lengths of SMRT reads enables multiple passes over each motif site. The reliability of the SMsn scores increases with more passes (i.e. higher single-molecule coverage).
- SMp: Single-molecule, motif-pooled analysis All motif sites on a sequencing molecule are pooled together and the molecule-wide methylation status for the given motif is assessed. This is designed for use with long (10Kb+) sequencing library preps, where each single long subread can span many distinct motif sites. The reliability of the SMp scores increases with increasing number of distinct motif sites contained in the subread.
There are three methods to install smalr on Debian 10. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install smalr Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install smalr using apt-get by running the following command:
sudo apt-get -y install smalr
Install smalr Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install smalr using apt by running the following command:
sudo apt -y install smalr
Install smalr 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 smalr using aptitude by running the following command:
sudo aptitude -y install smalr
How To Uninstall smalr on Debian 10
To uninstall only the smalr package we can use the following command:
sudo apt-get remove smalr
Uninstall smalr And Its Dependencies
To uninstall smalr and its dependencies that are no longer needed by Debian 10, we can use the command below:
sudo apt-get -y autoremove smalr
Remove smalr Configurations and Data
To remove smalr configuration and data from Debian 10 we can use the following command:
sudo apt-get -y purge smalr
Remove smalr configuration, data, and all of its dependencies
We can use the following command to remove smalr configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge smalr
Dependencies
smalr have the following dependencies:
References
Summary
In this tutorial we learn how to install smalr package on Debian 10 using different package management tools: apt, apt-get and aptitude.