How To Install rockhopper on Debian 12
Introduction
In this tutorial we learn how to install rockhopper on Debian 12.
What is rockhopper
rockhopper is:
Rockhopper is a comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data. As input, Rockhopper takes RNA sequencing reads output by high-throughput sequencing technology (FASTQ, QSEQ, FASTA, SAM, or BAM files). Rockhopper supports the following tasks:
- Reference based transcript assembly (when one or more reference
genomes are available)
- Aligning reads to genomes
- Assembling transcripts
- Identifying transcript boundaries and novel transcripts such as small RNAs
- De novo transcript assembly (when reference genomes are unavailable)
- Normalizing data from different experiments
- Quantifying transcript abundance
- Testing for differential gene expression
- Characterizing operon structures
- Visualizing results in a genome browser
There are three methods to install rockhopper 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 rockhopper Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install rockhopper using apt-get by running the following command:
sudo apt-get -y install rockhopper
Install rockhopper Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install rockhopper using apt by running the following command:
sudo apt -y install rockhopper
Install rockhopper 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 rockhopper using aptitude by running the following command:
sudo aptitude -y install rockhopper
How To Uninstall rockhopper on Debian 12
To uninstall only the rockhopper package we can use the following command:
sudo apt-get remove rockhopper
Uninstall rockhopper And Its Dependencies
To uninstall rockhopper and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove rockhopper
Remove rockhopper Configurations and Data
To remove rockhopper configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge rockhopper
Remove rockhopper configuration, data, and all of its dependencies
We can use the following command to remove rockhopper configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge rockhopper
Dependencies
rockhopper have the following dependencies:
References
Summary
In this tutorial we learn how to install rockhopper package on Debian 12 using different package management tools: apt, apt-get and aptitude.
