How To Install topp on Ubuntu

Posted on April 1, 2023 (Last modified on May 20, 2023 )

3 minutes • 498 words

Introduction

In this tutorial we learn how to install topp on Ubuntu.

What is `topp`

topp is:

TOPP (the OpenMS proteomic pipeline) is a pipeline for the analysis of HPLC/MS data. It consists of a set of numerous small applications that can be chained together to create analysis pipelines tailored for a specific problem. The applications make use of the libopenms library. Some examples of these applications are :

TOPPView: A viewer for mass spectrometry data.
TOPPAS: An assistant for GUI-driven TOPP workflow design.
DTAExtractor: Extracts spectra of an MS run file to several files in DTA format.
FileConverter: Converts between different MS file formats.
FileFilter: Extracts or manipulates portions of data from peak, feature or consensus feature files.
SpectraMerger: Merges spectra from an LC/MS map, either by precursor or by RT blocks.
BaselineFilter: Removes the baseline from profile spectra using a top-hat filter.
InternalCalibration: Applies an internal calibration.
PTModel: Trains a model for the prediction of proteotypic peptides from a training set.
RTPredict: Predicts retention times for peptides using a model trained by RTModel.
ExecutePipeline: Executes workflows created by TOPPAS.

There are three methods to install topp on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install topp Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install topp using apt-get by running the following command:

sudo apt-get -y install topp

Install topp Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install topp using apt by running the following command:

sudo apt -y install topp

Install topp 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 topp using aptitude by running the following command:

sudo aptitude -y install topp

How To Uninstall topp on Ubuntu

To uninstall only the topp package we can use the following command:

sudo apt-get remove topp

Uninstall topp And Its Dependencies

To uninstall topp and its dependencies that are no longer needed by Ubuntu, we can use the command below:

sudo apt-get -y autoremove topp

Remove topp Configurations and Data

To remove topp configuration and data from Ubuntu we can use the following command:

sudo apt-get -y purge topp

Remove topp configuration, data, and all of its dependencies

We can use the following command to remove topp configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge topp

Dependencies

topp have the following dependencies:

References

topp website

Summary

In this tutorial we learn how to install topp package on Ubuntu using different package management tools: apt, apt-get and aptitude.