How To Install tandem-mass-dbg on Debian 9
Introduction
In this tutorial we learn how to install tandem-mass-dbg on Debian 9.
What is tandem-mass-dbg
tandem-mass-dbg is:
X! Tandem can match tandem mass spectra with peptide sequences, in a process that is commonly used to perform protein identification.
This software has a very simple, unsophisticated application programming interface (API): it simply takes an XML file of instructions on its command line, and outputs the results into an XML file, which has been specified in the input XML file. The output file format is described at http://www.thegpm.org/docs/X_series_output_form.pdf
Unlike some earlier generation search engines, all of the X! Series search engines calculate statistical confidence (expectation values) for all of the individual spectrum-to-sequence assignments. They also reassemble all of the peptide assignments in a data set onto the known protein sequences and assign the statistical confidence that this assembly and alignment is non-random. The formula for which can be found here. Therefore, separate assembly and statistical analysis software, e.g. PeptideProphet and ProteinProphet, do not need to be used.
This package provides the debugging symbols for tandem-mass.
There are three methods to install tandem-mass-dbg 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 tandem-mass-dbg Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install tandem-mass-dbg using apt-get by running the following command:
sudo apt-get -y install tandem-mass-dbg
Install tandem-mass-dbg Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install tandem-mass-dbg using apt by running the following command:
sudo apt -y install tandem-mass-dbg
Install tandem-mass-dbg 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 tandem-mass-dbg using aptitude by running the following command:
sudo aptitude -y install tandem-mass-dbg
How To Uninstall tandem-mass-dbg on Debian 9
To uninstall only the tandem-mass-dbg package we can use the following command:
sudo apt-get remove tandem-mass-dbg
Uninstall tandem-mass-dbg And Its Dependencies
To uninstall tandem-mass-dbg and its dependencies that are no longer needed by Debian 9, we can use the command below:
sudo apt-get -y autoremove tandem-mass-dbg
Remove tandem-mass-dbg Configurations and Data
To remove tandem-mass-dbg configuration and data from Debian 9 we can use the following command:
sudo apt-get -y purge tandem-mass-dbg
Remove tandem-mass-dbg configuration, data, and all of its dependencies
We can use the following command to remove tandem-mass-dbg configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge tandem-mass-dbg
Dependencies
tandem-mass-dbg have the following dependencies:
References
Summary
In this tutorial we learn how to install tandem-mass-dbg package on Debian 9 using different package management tools: apt, apt-get and aptitude.
