How To Install ecopcr on Ubuntu 20.04
Introduction
In this tutorial we learn how to install ecopcr
on Ubuntu 20.04.
What is ecopcr
ecopcr is:
DNA barcoding is a tool for characterizing the species origin using a short sequence from a standard position and agreed upon position in the genome. To be used as a DNA barcode, a genome locus should vary among individuals of the same species only to a minor degree and it should vary among species very quickly. From a practical point of view, a barcode locus should be flanked by two conserved regions to design PCR primers. Several manually discovered barcode loci like COI, rbcL, 18S, 16S and 23S rDNA, or trnH-ps are routinely used today, but no objective function has been described to measure their quality in terms of universality (barcode coverage, Bc ) or in terms of taxonomical discrimination capacity (barcode specificity, Bs ).
ecoPCR is an electronic PCR software developed by LECA and Helix-Project. It helps to estimate Barcode primers quality. In conjunction with OBITools you can postprocess ecoPCR output to compute barcode coverage and barcode specificity. New barcode primers can be developed using the ecoPrimers software
There are three methods to install ecopcr
on Ubuntu 20.04. We can use apt-get
, apt
and aptitude
. In the following sections we will describe each method. You can choose one of them.
Install ecopcr Using apt-get
Update apt database with apt-get
using the following command.
sudo apt-get update
After updating apt database, We can install ecopcr
using apt-get
by running the following command:
sudo apt-get -y install ecopcr
Install ecopcr Using apt
Update apt database with apt
using the following command.
sudo apt update
After updating apt database, We can install ecopcr
using apt
by running the following command:
sudo apt -y install ecopcr
Install ecopcr 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 ecopcr
using aptitude
by running the following command:
sudo aptitude -y install ecopcr
How To Uninstall ecopcr on Ubuntu 20.04
To uninstall only the ecopcr
package we can use the following command:
sudo apt-get remove ecopcr
Uninstall ecopcr And Its Dependencies
To uninstall ecopcr
and its dependencies that are no longer needed by Ubuntu 20.04, we can use the command below:
sudo apt-get -y autoremove ecopcr
Remove ecopcr Configurations and Data
To remove ecopcr
configuration and data from Ubuntu 20.04 we can use the following command:
sudo apt-get -y purge ecopcr
Remove ecopcr configuration, data, and all of its dependencies
We can use the following command to remove ecopcr
configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge ecopcr
References
Summary
In this tutorial we learn how to install ecopcr
package on Ubuntu 20.04 using different package management tools: apt
, apt-get
and aptitude
.