How To Install staden-common on Ubuntu 18.04
Introduction
In this tutorial we learn how to install staden-common on Ubuntu 18.04.
What is staden-common
staden-common is:
Staden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin).
Gap4 performs sequence assembly, contig ordering based on read pair data, contig joining based on sequence comparisons, assembly checking, repeat searching, experiment suggestion, read pair analysis and contig editing. It has graphical views of contigs, templates, readings and traces which all scroll in register. Contig editor searches and experiment suggestion routines use confidence values to calculate the confidence of the consensus sequence and hence identify only places requiring visual trace inspection or extra data. The result is extremely rapid finishing and a consensus of known accuracy.
Pregap4 provides a graphical user interface to set up the processing required to prepare trace data for assembly or analysis, and automates these processes.
Trev is a rapid and flexible viewer and editor for ABI, ALF, SCF and ZTR trace files.
Prefinish analyses partially completed sequence assemblies and suggests the most efficient set of experiments to help finish the project.
Tracediff and hetscan automatically locate mutations by comparing trace data against reference traces. They annotate the mutations found ready for viewing in gap4.
Spin analyses nucleotide sequences to find genes, restriction sites, motifs, etc. It can perform translations, find open reading frames, count codons, etc. Many results are presented graphically and a sliding sequence window is linked to the graphics cursor. Spin also compares pairs of sequences in many ways. It has very rapid dot matrix analysis, global and local alignment algorithms, plus a sliding sequence window linked to the graphical plots. It can compare nucleic acid against nucleic acid, protein against protein, and protein against nucleic acid.
This package contains the architecture independent data files and scripts that come with the Staden package.
There are three methods to install staden-common 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 staden-common Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install staden-common using apt-get by running the following command:
sudo apt-get -y install staden-common
Install staden-common Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install staden-common using apt by running the following command:
sudo apt -y install staden-common
Install staden-common 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 staden-common using aptitude by running the following command:
sudo aptitude -y install staden-common
How To Uninstall staden-common on Ubuntu 18.04
To uninstall only the staden-common package we can use the following command:
sudo apt-get remove staden-common
Uninstall staden-common And Its Dependencies
To uninstall staden-common and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove staden-common
Remove staden-common Configurations and Data
To remove staden-common configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge staden-common
Remove staden-common configuration, data, and all of its dependencies
We can use the following command to remove staden-common configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge staden-common
References
Summary
In this tutorial we learn how to install staden-common package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
