How To Install percolator on CentOS 8
Introduction
In this tutorial we learn how to install percolator on CentOS 8.
What is percolator
The first step in analyzing an mass spectrometry assay is to match the harvested spectra against a target database using database search engines such as Sequest and Mascot, a process that renders list of peptide-spectrum matches. However, it is not trivial to assess the accuracy of these identifications. Percolator uses a semi-supervised machine learning to discriminate correct from incorrect peptide-spectrum matches, and calculates accurate statistics such as q-value (FDR) and posterior error probabilities.
We can use yum or dnf to install percolator on CentOS 8. In this tutorial we discuss both methods but you only need to choose one of method to install percolator.
Install percolator on CentOS 8 Using dnf
Update yum database with dnf using the following command.
sudo dnf makecache --refresh
The output should look something like this:
CentOS Linux 8 - AppStream 43 kB/s | 4.3 kB 00:00
CentOS Linux 8 - BaseOS 65 kB/s | 3.9 kB 00:00
CentOS Linux 8 - ContinuousRelease 43 kB/s | 3.0 kB 00:00
CentOS Linux 8 - Extras 23 kB/s | 1.5 kB 00:00
CentOS Linux 8 - FastTrack 40 kB/s | 3.0 kB 00:00
CentOS Linux 8 - HighAvailability 36 kB/s | 3.9 kB 00:00
CentOS Linux 8 - Plus 24 kB/s | 1.5 kB 00:00
CentOS Linux 8 - PowerTools 50 kB/s | 4.3 kB 00:00
Extra Packages for Enterprise Linux Modular 8 - x86_64 13 kB/s | 9.2 kB 00:00
Extra Packages for Enterprise Linux 8 - x86_64 24 kB/s | 8.5 kB 00:00
Metadata cache created.
After updating yum database, We can install percolator using dnf by running the following command:
sudo dnf -y install percolator
Install percolator on CentOS 8 Using yum
Update yum database with yum using the following command.
sudo yum makecache --refresh
The output should look something like this:
CentOS Linux 8 - AppStream 43 kB/s | 4.3 kB 00:00
CentOS Linux 8 - BaseOS 65 kB/s | 3.9 kB 00:00
CentOS Linux 8 - ContinuousRelease 43 kB/s | 3.0 kB 00:00
CentOS Linux 8 - Extras 23 kB/s | 1.5 kB 00:00
CentOS Linux 8 - FastTrack 40 kB/s | 3.0 kB 00:00
CentOS Linux 8 - HighAvailability 36 kB/s | 3.9 kB 00:00
CentOS Linux 8 - Plus 24 kB/s | 1.5 kB 00:00
CentOS Linux 8 - PowerTools 50 kB/s | 4.3 kB 00:00
Extra Packages for Enterprise Linux Modular 8 - x86_64 13 kB/s | 9.2 kB 00:00
Extra Packages for Enterprise Linux 8 - x86_64 24 kB/s | 8.5 kB 00:00
Metadata cache created.
After updating yum database, We can install percolator using yum by running the following command:
sudo yum -y install percolator
How To Uninstall percolator on CentOS 8
To uninstall only the percolator package we can use the following command:
sudo dnf remove percolator
percolator Package Contents on CentOS 8
/usr/bin/elude
/usr/bin/msgf2pin
/usr/bin/percolator
/usr/bin/qvality
/usr/bin/sqt2pin
/usr/bin/tandem2pin
/usr/lib/.build-id
/usr/lib/.build-id/3d
/usr/lib/.build-id/3d/f5b3b0d656821958e1dfbcac84807593310f51
/usr/lib/.build-id/56
/usr/lib/.build-id/56/3e90b6c7229f381c59ba2ead8ee215ef497e0a
/usr/lib/.build-id/7c
/usr/lib/.build-id/7c/1e7b48f002bef526c83beadcac3d92914d3156
/usr/lib/.build-id/b9
/usr/lib/.build-id/b9/11ee11f4177deda6f4ab327727ddd7595dea6e
/usr/lib/.build-id/f1
/usr/lib/.build-id/f1/78932af23ea4593b57469ddc145276669f3561
/usr/lib/.build-id/f3
/usr/lib/.build-id/f3/f7c5782af2e9b1429469d53a61e6177a61d2b7
References
Summary
In this tutorial we learn how to install percolator on CentOS 8 using yum and dnf.