How To Install ruby-crb-blast on Ubuntu 18.04
Introduction
In this tutorial we learn how to install ruby-crb-blast on Ubuntu 18.04.
What is ruby-crb-blast
ruby-crb-blast is:
CRB-BLAST is a novel method for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation.
CRB-BLAST initially performs a standard reciprocal best BLAST. It does this by performing BLAST alignments of query->target and target->query. Reciprocal best BLAST hits are those where the best match for any given query sequence in the query->target alignment is also the best hit of the match in the reverse (target->query) alignment.
Reciprocal best BLAST is a very conservative way to assign orthologs. The main innovation in CRB-BLAST is to learn an appropriate e-value cutoff to apply to each pairwise alignment by taking into account the overall relatedness of the two datasets being compared. This is done by fitting a function to the distribution of alignment e-values over sequence lengths. The function provides the e-value cutoff for a sequence of given length.
There are three methods to install ruby-crb-blast on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install ruby-crb-blast Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install ruby-crb-blast using apt-get by running the following command:
sudo apt-get -y install ruby-crb-blast
Install ruby-crb-blast Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install ruby-crb-blast using apt by running the following command:
sudo apt -y install ruby-crb-blast
Install ruby-crb-blast 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 Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install ruby-crb-blast using aptitude by running the following command:
sudo aptitude -y install ruby-crb-blast
How To Uninstall ruby-crb-blast on Ubuntu 18.04
To uninstall only the ruby-crb-blast package we can use the following command:
sudo apt-get remove ruby-crb-blast
Uninstall ruby-crb-blast And Its Dependencies
To uninstall ruby-crb-blast and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove ruby-crb-blast
Remove ruby-crb-blast Configurations and Data
To remove ruby-crb-blast configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge ruby-crb-blast
Remove ruby-crb-blast configuration, data, and all of its dependencies
We can use the following command to remove ruby-crb-blast configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge ruby-crb-blast
References
Summary
In this tutorial we learn how to install ruby-crb-blast package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
