How To Install r-bioc-genomicalignments on Debian 9
Introduction
In this tutorial we learn how to install r-bioc-genomicalignments
on Debian 9.
What is r-bioc-genomicalignments
r-bioc-genomicalignments is:
This BioConductor package provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.
There are three methods to install r-bioc-genomicalignments
on Debian 9. We can use apt-get
, apt
and aptitude
. In the following sections we will describe each method. You can choose one of them.
Install r-bioc-genomicalignments Using apt-get
Update apt database with apt-get
using the following command.
sudo apt-get update
After updating apt database, We can install r-bioc-genomicalignments
using apt-get
by running the following command:
sudo apt-get -y install r-bioc-genomicalignments
Install r-bioc-genomicalignments Using apt
Update apt database with apt
using the following command.
sudo apt update
After updating apt database, We can install r-bioc-genomicalignments
using apt
by running the following command:
sudo apt -y install r-bioc-genomicalignments
Install r-bioc-genomicalignments 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 r-bioc-genomicalignments
using aptitude
by running the following command:
sudo aptitude -y install r-bioc-genomicalignments
How To Uninstall r-bioc-genomicalignments on Debian 9
To uninstall only the r-bioc-genomicalignments
package we can use the following command:
sudo apt-get remove r-bioc-genomicalignments
Uninstall r-bioc-genomicalignments And Its Dependencies
To uninstall r-bioc-genomicalignments
and its dependencies that are no longer needed by Debian 9, we can use the command below:
sudo apt-get -y autoremove r-bioc-genomicalignments
Remove r-bioc-genomicalignments Configurations and Data
To remove r-bioc-genomicalignments
configuration and data from Debian 9 we can use the following command:
sudo apt-get -y purge r-bioc-genomicalignments
Remove r-bioc-genomicalignments configuration, data, and all of its dependencies
We can use the following command to remove r-bioc-genomicalignments
configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-bioc-genomicalignments
Dependencies
r-bioc-genomicalignments have the following dependencies:
- r-base-core
- r-api-3
- r-bioc-biocgenerics
- r-bioc-s4vectors
- r-bioc-iranges
- r-bioc-genomeinfodb
- r-bioc-genomicranges
- r-bioc-summarizedexperiment
- r-bioc-biostrings
- r-bioc-rsamtools
- r-bioc-biocparallel
- libc6
References
Summary
In this tutorial we learn how to install r-bioc-genomicalignments
package on Debian 9 using different package management tools: apt
, apt-get
and aptitude
.