How To Install openms on Fedora 34

openms is LC/MS data management and analyses LC/MS data management and analyses

Introduction

In this tutorial we learn how to install openms on Fedora 34.

What is `openms`

OpenMS is a C++ library for LC-MS data management and analyses. It offers an infrastructure for the rapid development of mass spectrometry related software. OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux. It comes with a vast variety of pre-built and ready-to-use tools for proteomics and metabolomics data analysis (TOPPTools) and powerful 2D and 3D visualization(TOPPView). OpenMS offers analyses for various quantitation protocols, including label-free quantitation, SILAC, iTRAQ, SRM, SWATH, etc. It provides built-in algorithms for de-novo identification and database search, as well as adapters to other state-of-the art tools like XTandem, Mascot, OMSSA, etc. It supports easy integration of OpenMS built tools into workflow engines like Knime, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and a unified parameter handling via a ‘common tool description’ (CTD) scheme. The OpenMS Proteomics Pipeline is a pipeline for the analysis of HPLC-MS data. It consists of several small applications that can be chained to create analysis pipelines tailored for a specific problem. The TOPP tools are divided into several subgroups - Graphical Tools - File Handling - Signal Processing and Preprocessing - Quantitation - Map Alignment - Protein/Peptide Identification - Protein/Peptide Processing - Targeted Experiments - Peptide Property Prediction - Misc openms 2.6.0 7.fc34 x86_64 9.9 M openms-2.6.0-7.fc34.src.rpm updates LC/MS data management and analyses http BSD OpenMS is a C++ library for LC-MS data management and analyses. It offers an infrastructure for the rapid development of mass spectrometry related software. OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux. It comes with a vast variety of pre-built and ready-to-use tools for proteomics and metabolomics data analysis (TOPPTools) and powerful 2D and 3D visualization(TOPPView). OpenMS offers analyses for various quantitation protocols, including label-free quantitation, SILAC, iTRAQ, SRM, SWATH, etc. It provides built-in algorithms for de-novo identification and database search, as well as adapters to other state-of-the art tools like XTandem, Mascot, OMSSA, etc. It supports easy integration of OpenMS built tools into workflow engines like Knime, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and a unified parameter handling via a ‘common tool description’ (CTD) scheme. The OpenMS Proteomics Pipeline is a pipeline for the analysis of HPLC-MS data. It consists of several small applications that can be chained to create analysis pipelines tailored for a specific problem. The TOPP tools are divided into several subgroups - Graphical Tools - File Handling - Signal Processing and Preprocessing - Quantitation - Map Alignment - Protein/Peptide Identification - Protein/Peptide Processing - Targeted Experiments - Peptide Property Prediction - Misc

We can use yum or dnf to install openms on Fedora 34. In this tutorial we discuss both methods but you only need to choose one of method to install openms.

Install openms on Fedora 34 Using dnf

Update yum database with dnf using the following command.

sudo dnf makecache --refresh

The output should look something like this:

Fedora 34 - x86_64                               20 kB/s | 6.6 kB     00:00
Fedora 34 openh264 (From Cisco) - x86_64        1.4 kB/s | 989  B     00:00
Fedora Modular 34 - x86_64                       68 kB/s | 6.5 kB     00:00
Fedora 34 - x86_64 - Updates                    3.5 kB/s | 6.2 kB     00:01
Fedora Modular 34 - x86_64 - Updates             17 kB/s | 5.9 kB     00:00
Metadata cache created.

After updating yum database, We can install openms using dnf by running the following command:

sudo dnf -y install openms

Install openms on Fedora 34 Using yum

Update yum database with yum using the following command.

sudo yum makecache --refresh

The output should look something like this:

Fedora 34 - x86_64                               20 kB/s | 6.6 kB     00:00
Fedora 34 openh264 (From Cisco) - x86_64        1.4 kB/s | 989  B     00:00
Fedora Modular 34 - x86_64                       68 kB/s | 6.5 kB     00:00
Fedora 34 - x86_64 - Updates                    3.5 kB/s | 6.2 kB     00:01
Fedora Modular 34 - x86_64 - Updates             17 kB/s | 5.9 kB     00:00
Metadata cache created.

After updating yum database, We can install openms using yum by running the following command:

sudo yum -y install openms

How To Uninstall openms on Fedora 34

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

sudo dnf remove openms

openms Package Contents on Fedora 34

/usr/bin/BaselineFilter
/usr/bin/CompNovo
/usr/bin/CompNovoCID
/usr/bin/ConsensusID
/usr/bin/ConsensusMapNormalizer
/usr/bin/DTAExtractor
/usr/bin/DatabaseFilter
/usr/bin/DatabaseSuitability
/usr/bin/Decharger
/usr/bin/EICExtractor
/usr/bin/ExecutePipeline
/usr/bin/FalseDiscoveryRate
/usr/bin/FeatureFinderCentroided
/usr/bin/FeatureFinderIdentification
/usr/bin/FeatureFinderIsotopeWavelet
/usr/bin/FeatureFinderMRM
/usr/bin/FeatureFinderMetabo
/usr/bin/FeatureFinderMultiplex
/usr/bin/FeatureLinkerLabeled
/usr/bin/FeatureLinkerUnlabeled
/usr/bin/FeatureLinkerUnlabeledKD
/usr/bin/FeatureLinkerUnlabeledQT
/usr/bin/FidoAdapter
/usr/bin/FileConverter
/usr/bin/FileInfo
/usr/bin/FileMerger
/usr/bin/GenericWrapper
/usr/bin/HighResPrecursorMassCorrector
/usr/bin/IDConflictResolver
/usr/bin/IDFileConverter
/usr/bin/IDFilter
/usr/bin/IDMapper
/usr/bin/IDMerger
/usr/bin/IDPosteriorErrorProbability
/usr/bin/IDRTCalibration
/usr/bin/IDRipper
/usr/bin/IDScoreSwitcher
/usr/bin/INIFileEditor
/usr/bin/InclusionExclusionListCreator
/usr/bin/InspectAdapter
/usr/bin/InternalCalibration
/usr/bin/IsobaricAnalyzer
/usr/bin/LuciphorAdapter
/usr/bin/MRMMapper
/usr/bin/MRMTransitionGroupPicker
/usr/bin/MSGFPlusAdapter
/usr/bin/MapAlignerIdentification
/usr/bin/MapAlignerPoseClustering
/usr/bin/MapAlignerSpectrum
/usr/bin/MapNormalizer
/usr/bin/MapRTTransformer
/usr/bin/MapStatistics
/usr/bin/MascotAdapter
/usr/bin/MascotAdapterOnline
/usr/bin/MassTraceExtractor
/usr/bin/MetaProSIP
/usr/bin/MetaboliteSpectralMatcher
/usr/bin/MyriMatchAdapter
/usr/bin/MzMLSplitter
/usr/bin/MzTabExporter
/usr/bin/NoiseFilterGaussian
/usr/bin/NoiseFilterSGolay
/usr/bin/OMSSAAdapter
/usr/bin/OpenSwathAnalyzer
/usr/bin/OpenSwathAssayGenerator
/usr/bin/OpenSwathChromatogramExtractor
/usr/bin/OpenSwathConfidenceScoring
/usr/bin/OpenSwathDecoyGenerator
/usr/bin/OpenSwathFeatureXMLToTSV
/usr/bin/OpenSwathRTNormalizer
/usr/bin/OpenSwathWorkflow
/usr/bin/PTModel
/usr/bin/PTPredict
/usr/bin/PeakPickerHiRes
/usr/bin/PeakPickerIterative
/usr/bin/PeakPickerWavelet
/usr/bin/PepNovoAdapter
/usr/bin/PeptideIndexer
/usr/bin/PercolatorAdapter
/usr/bin/PrecursorIonSelector
/usr/bin/PrecursorMassCorrector
/usr/bin/ProteinInference
/usr/bin/ProteinQuantifier
/usr/bin/ProteinResolver
/usr/bin/RNPxlSearch
/usr/bin/RTModel
/usr/bin/RTPredict
/usr/bin/Resampler
/usr/bin/SeedListGenerator
/usr/bin/SimpleSearchEngine
/usr/bin/SpecLibSearcher
/usr/bin/SpectraFilterBernNorm
/usr/bin/SpectraFilterMarkerMower
/usr/bin/SpectraFilterNLargest
/usr/bin/SpectraFilterNormalizer
/usr/bin/SpectraFilterParentPeakMower
/usr/bin/SpectraFilterScaler
/usr/bin/SpectraFilterSqrtMower
/usr/bin/SpectraFilterThresholdMower
/usr/bin/SpectraFilterWindowMower
/usr/bin/SpectraMerger
/usr/bin/StaticModification
/usr/bin/SwathWizard
/usr/bin/TOFCalibration
/usr/bin/TOPPAS
/usr/bin/TOPPView
/usr/bin/TextExporter
/usr/bin/XTandemAdapter
/usr/lib/.build-id
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/usr/share/icons/TOPP/pixmaps
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/usr/share/metainfo/TOPPView.appdata.xml
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/usr/bin/DatabaseSuitability
/usr/bin/Decharger
/usr/bin/EICExtractor
/usr/bin/ExecutePipeline
/usr/bin/FalseDiscoveryRate
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/usr/lib64/OpenMS
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/usr/lib64/OpenMS/libOpenSwathAlgo.so
/usr/lib64/OpenMS/libSuperHirn.so
/usr/share/applications/TOPPAS.desktop
/usr/share/applications/TOPPView.desktop
/usr/share/applications/inifileeditor.desktop
/usr/share/icons/TOPP
/usr/share/icons/TOPP/INIFileEditor.png
/usr/share/icons/TOPP/TOPPAS.png
/usr/share/icons/TOPP/TOPPView.png
/usr/share/icons/TOPP/pixmaps
/usr/share/metainfo/TOPPAS.appdata.xml
/usr/share/metainfo/TOPPView.appdata.xml

References

[openms website](http://www.openms.de/ http://www.openms.de/)

Summary

In this tutorial we learn how to install openms on Fedora 34 using yum and dnf.