Release notes 2017 08

Michael van Vliet edited this page Aug 18, 2017 · 25 revisions

The 2017-08 release of PhenoMeNal, also known as “Bucetin”, was released mid August 16th. It represents a major upgrade to the 2017-02 beta release. It has a richer set of tools, depends on improved deployment software, includes workflows for MS and NMR, and is no longer considered beta. Tools also had too pass more stringent testing to be included, compared to the beta release. The same is true for workflows.

The main user facing components of the release are:

The main deployment components of the release are:

PhenoMeNal Galaxy workflow environment

The Bucetine release of the PhenoMeNal Galaxy container includes:

  • >150 Galaxy tools, based on more than >50 containers, including
    • 7 NMR Tools
    • 26 MS Tools (plus 97 MS tools from OpenMS)
    • 14 Data transfer/ISA processing tools.
    • 6 Statistics tools.
  • 4 Workflows pre-assembled as example
    • Fluxomics 13C-labeled MS Workflow
    • 1D NMR Workflow
    • LC-MS/MS XCMS-Metfrag Workflow
    • Multi-omics univariate/multivariate analysis Workflow (W4M)

More details available on the PhenoMeNal Galaxy container README file

PhenoMeNal Gateway Portal

The PhenoMeNal Gateway Portal Bucetine release includes:

  • Development of User Audit Metadata Storage
  • Containerisation of PhenoMeNal Portal Components
    • The App Library
    • The Wiki
    • The PhenoMeNal Portal Frontend
    • User Audit Metadata Storage
    • User Audit Database
  • Fully deployable on Kubernetes through Portal helm charts
  • OpenStack API Integration into PhenoMeNal Portal (this will be enabled in short time)

Cloud deploy KubeNow

Cloud deployment backend of PhenoMeNal Gateway Portal and standalone Command Line Client for rapid and customized deployment of PhenoMeNal CRE

  • Supports Amazon Web Services, Google Cloud Platform and OpenStack
  • Simple usage via Dockerzed command line client
  • Extended logging capabilities

KubeNow

  • A Kubernetes cluster up and running in less than 10 minutes (provisioned with kubeadm)
  • Supports deployment on Amazon Web Services, Google Cloud Platform and OpenStack
  • Simple usage via Dockerzed command line client
  • Weave networking
  • Traefik HTTP reverse proxy and load balancer
  • Cloudflare dynamic DNS integration
  • GlusterFS distributed file system

Galaxy Helm Chart

A Helm chart for deploying Galaxy on Kubernetes clusters and local minikube installations (mostly for development):

  • Support for production and development environments
  • Support for Postgresql or SQLite deployment
  • Injection of user setup and other environment variables

Galaxy Tool versions

Section Category Tool Version
Generic Get Data upload
Generic Text Manipulation fixedValueColumn
Generic Text Manipulation catWrapper
Generic Text Manipulation condense_characters
Generic Text Manipulation convert_characters
Generic Text Manipulation mergeCols
Generic Text Manipulation CreateInterval
Generic Text Manipulation cutWrapper
Generic Text Manipulation changeCase
Generic Text Manipulation pasteWrapper
Generic Text Manipulation remove_beginning
Generic Text Manipulation randomlines
Generic Text Manipulation headWrapper
Generic Text Manipulation tailWrapper
Generic Text Manipulation trimmer
Generic Text Manipulation wc_gnu
Generic Text Manipulation secure_hash_message_digest
Generic Filter and Sort filtering
Generic Filter and Sort sorter
Generic Filter and Sort grep
Generic Join, Subtract and Group joiner
Generic Join, Subtract and Group compare
Generic Join, Subtract and Group grouping
Generic Join, Subtract and Group zip-collection 0.1
Generic Statistics gsummary
Generic Statistics uniq
Generic Graph/Display Data boxplot
PhenoMeNal H2020 Tools Transfer metabolights-downloader 0.1.0
PhenoMeNal H2020 Tools Transfer metabolights-labs-uploader 0.1.0
PhenoMeNal H2020 Tools Fluxomics ramid 0.1.0
PhenoMeNal H2020 Tools Fluxomics midcor 0.1.0
PhenoMeNal H2020 Tools Fluxomics iso2flux 1.0
PhenoMeNal H2020 Tools Fluxomics isodyn 0.1.0
PhenoMeNal H2020 Tools Fluxomics fluxomics-viz 0.1
PhenoMeNal H2020 Tools NMR mtbls_nmr_raw_dummy_importer 0.4
PhenoMeNal H2020 Tools NMR nmrmlconv 0.4
PhenoMeNal H2020 Tools NMR zip-nmrml-collection 0.4
PhenoMeNal H2020 Tools NMR rnmr1d 0.4
PhenoMeNal H2020 Tools NMR rnmr1d-stacked-plot 0.4
PhenoMeNal H2020 Tools NMR batman
PhenoMeNal H2020 Tools NMR metabomatching
PhenoMeNal H2020 Tools NMR nmrml2isa 0.1.0
PhenoMeNal H2020 Tools NMR mtbls2nmrglue 1.0
PhenoMeNal H2020 Tools NMR soap_process 1.0
PhenoMeNal H2020 Tools NMR soap_opls 1.0
PhenoMeNal H2020 Tools STATS papy
PhenoMeNal H2020 Tools MS save_chromatogram 1.1
PhenoMeNal H2020 Tools MS show_chromatogram 1.1
PhenoMeNal H2020 Tools MS mzml2isa 0.1.0
PhenoMeNal H2020 Tools MS metfrag 0.2
PhenoMeNal H2020 Tools MS ms-vfetc 0.1.1
PhenoMeNal H2020 Tools MS xcms-find-peaks 0.1
PhenoMeNal H2020 Tools MS xcms-split-peaks 0.1
PhenoMeNal H2020 Tools MS xcms-collect-peaks 0.1
PhenoMeNal H2020 Tools MS xcms-group-peaks 0.1
PhenoMeNal H2020 Tools MS xcms-correct-rt 0.1
PhenoMeNal H2020 Tools MS xcms-fill-peaks 0.1
PhenoMeNal H2020 Tools MS camera-annotate-peaks 0.1
PhenoMeNal H2020 Tools MS camera-group-fwhm 0.1
PhenoMeNal H2020 Tools MS camera-group-corr 0.1
PhenoMeNal H2020 Tools MS camera-find-isotopes 0.1
PhenoMeNal H2020 Tools MS camera-find-adducts 0.1
PhenoMeNal H2020 Tools MS msnbase-read-msms 0.1
PhenoMeNal H2020 Tools MS map-msms2camera 0.1
PhenoMeNal H2020 Tools MS msms2metfrag 0.1
PhenoMeNal H2020 Tools MS metfrag-cli-batch 0.1
PhenoMeNal H2020 Tools MS metfrag-vis 0.1
PhenoMeNal H2020 Tools MS AdditiveSeries 2.1.0
PhenoMeNal H2020 Tools MS BaselineFilter 2.1.0
PhenoMeNal H2020 Tools MS CompNovo 2.1.0
PhenoMeNal H2020 Tools MS CompNovoCID 2.1.0
PhenoMeNal H2020 Tools MS ConsensusID 2.1.0
PhenoMeNal H2020 Tools MS ConsensusMapNormalizer 2.1.0
PhenoMeNal H2020 Tools MS Decharger 2.1.0
PhenoMeNal H2020 Tools MS DTAExtractor 2.1.0
PhenoMeNal H2020 Tools MS EICExtractor 2.1.0
PhenoMeNal H2020 Tools MS ExternalCalibration 2.1.0
PhenoMeNal H2020 Tools MS FalseDiscoveryRate 2.1.0
PhenoMeNal H2020 Tools MS FeatureFinderCentroided 2.1.0
PhenoMeNal H2020 Tools MS FeatureFinderIdentification 2.1.0
PhenoMeNal H2020 Tools MS FeatureFinderIsotopeWavelet 2.1.0
PhenoMeNal H2020 Tools MS FeatureFinderMetabo 2.1.0
PhenoMeNal H2020 Tools MS FeatureFinderMRM 2.1.0
PhenoMeNal H2020 Tools MS FeatureFinderMultiplex 2.1.0
PhenoMeNal H2020 Tools MS FeatureLinkerLabeled 2.1.0
PhenoMeNal H2020 Tools MS FeatureLinkerUnlabeled 2.1.0
PhenoMeNal H2020 Tools MS FeatureLinkerUnlabeledQT 2.1.0
PhenoMeNal H2020 Tools MS FidoAdapter 2.1.0
PhenoMeNal H2020 Tools MS FileConverter 2.1.0
PhenoMeNal H2020 Tools MS FileFilter 2.1.0
PhenoMeNal H2020 Tools MS FileInfo 2.1.0
PhenoMeNal H2020 Tools MS FileMerger 2.1.0
PhenoMeNal H2020 Tools MS HighResPrecursorMassCorrector 2.1.0
PhenoMeNal H2020 Tools MS IDConflictResolver 2.1.0
PhenoMeNal H2020 Tools MS IDFileConverter 2.1.0
PhenoMeNal H2020 Tools MS IDFilter 2.1.0
PhenoMeNal H2020 Tools MS IDMapper 2.1.0
PhenoMeNal H2020 Tools MS IDMerger 2.1.0
PhenoMeNal H2020 Tools MS IDPosteriorErrorProbability 2.1.0
PhenoMeNal H2020 Tools MS IDRipper 2.1.0
PhenoMeNal H2020 Tools MS IDRTCalibration 2.1.0
PhenoMeNal H2020 Tools MS InclusionExclusionListCreator 2.1.0
PhenoMeNal H2020 Tools MS InspectAdapter 2.1.0
PhenoMeNal H2020 Tools MS InternalCalibration 2.1.0
PhenoMeNal H2020 Tools MS IsobaricAnalyzer 2.1.0
PhenoMeNal H2020 Tools MS ITRAQAnalyzer 2.1.0
PhenoMeNal H2020 Tools MS LuciphorAdapter 2.1.0
PhenoMeNal H2020 Tools MS MapAlignerIdentification 2.1.0
PhenoMeNal H2020 Tools MS MapAlignerPoseClustering 2.1.0
PhenoMeNal H2020 Tools MS MapAlignerSpectrum 2.1.0
PhenoMeNal H2020 Tools MS MapNormalizer 2.1.0
PhenoMeNal H2020 Tools MS MapRTTransformer 2.1.0
PhenoMeNal H2020 Tools MS MapStatistics 2.1.0
PhenoMeNal H2020 Tools MS MascotAdapter 2.1.0
PhenoMeNal H2020 Tools MS MascotAdapterOnline 2.1.0
PhenoMeNal H2020 Tools MS MassTraceExtractor 2.1.0
PhenoMeNal H2020 Tools MS MRMMapper 2.1.0
PhenoMeNal H2020 Tools MS MSGFPlusAdapter 2.1.0
PhenoMeNal H2020 Tools MS MyriMatchAdapter 2.1.0
PhenoMeNal H2020 Tools MS MzTabExporter 2.1.0
PhenoMeNal H2020 Tools MS NoiseFilterGaussian 2.1.0
PhenoMeNal H2020 Tools MS NoiseFilterSGolay 2.1.0
PhenoMeNal H2020 Tools MS OMSSAAdapter 2.1.0
PhenoMeNal H2020 Tools MS OpenSwathAnalyzer 2.1.0
PhenoMeNal H2020 Tools MS OpenSwathAssayGenerator 2.1.0
PhenoMeNal H2020 Tools MS OpenSwathChromatogramExtractor 2.1.0
PhenoMeNal H2020 Tools MS OpenSwathConfidenceScoring 2.1.0
PhenoMeNal H2020 Tools MS OpenSwathDecoyGenerator 2.1.0
PhenoMeNal H2020 Tools MS OpenSwathFeatureXMLToTSV 2.1.0
PhenoMeNal H2020 Tools MS OpenSwathRTNormalizer 2.1.0
PhenoMeNal H2020 Tools MS PeakPickerHiRes 2.1.0
PhenoMeNal H2020 Tools MS PeakPickerWavelet 2.1.0
PhenoMeNal H2020 Tools MS PepNovoAdapter 2.1.0
PhenoMeNal H2020 Tools MS PeptideIndexer 2.1.0
PhenoMeNal H2020 Tools MS PhosphoScoring 2.1.0
PhenoMeNal H2020 Tools MS PrecursorIonSelector 2.1.0
PhenoMeNal H2020 Tools MS PrecursorMassCorrector 2.1.0
PhenoMeNal H2020 Tools MS ProteinInference 2.1.0
PhenoMeNal H2020 Tools MS ProteinQuantifier 2.1.0
PhenoMeNal H2020 Tools MS ProteinResolver 2.1.0
PhenoMeNal H2020 Tools MS PTModel 2.1.0
PhenoMeNal H2020 Tools MS PTPredict 2.1.0
PhenoMeNal H2020 Tools MS RTModel 2.1.0
PhenoMeNal H2020 Tools MS RTPredict 2.1.0
PhenoMeNal H2020 Tools MS SeedListGenerator 2.1.0
PhenoMeNal H2020 Tools MS SpecLibSearcher 2.1.0
PhenoMeNal H2020 Tools MS SpectraFilterBernNorm 2.1.0
PhenoMeNal H2020 Tools MS SpectraFilterMarkerMower 2.1.0
PhenoMeNal H2020 Tools MS SpectraFilterNLargest 2.1.0
PhenoMeNal H2020 Tools MS SpectraFilterNormalizer 2.1.0
PhenoMeNal H2020 Tools MS SpectraFilterParentPeakMower 2.1.0
PhenoMeNal H2020 Tools MS SpectraFilterScaler 2.1.0
PhenoMeNal H2020 Tools MS SpectraFilterSqrtMower 2.1.0
PhenoMeNal H2020 Tools MS SpectraFilterThresholdMower 2.1.0
PhenoMeNal H2020 Tools MS SpectraFilterWindowMower 2.1.0
PhenoMeNal H2020 Tools MS SpectraMerger 2.1.0
PhenoMeNal H2020 Tools MS TextExporter 2.1.0
PhenoMeNal H2020 Tools MS TMTAnalyzer 2.1.0
PhenoMeNal H2020 Tools MS TOFCalibration 2.1.0
PhenoMeNal H2020 Tools MS XTandemAdapter 2.1.0
PhenoMeNal H2020 Tools MS cameraToFeatureXML 1.0
PhenoMeNal H2020 Tools MS consensusXMLToXcms 1.0
PhenoMeNal H2020 Tools MS featureXMLToCAMERA 1.0
PhenoMeNal H2020 Tools MS featureXMLToXcms 1.0
PhenoMeNal H2020 Tools W4M mtbls-dwnld_config 2.0.5
PhenoMeNal H2020 Tools W4M univariate_config 2.2.3
PhenoMeNal H2020 Tools W4M multivariate_config 2.3.10
PhenoMeNal H2020 Tools W4M biosigner_config 2.2.7
PhenoMeNal H2020 Tools W4M lcmsmatching_config 3.1.6
PhenoMeNal H2020 Tools Post-Processing metaboliteidconverter 0.4
PhenoMeNal H2020 Tools ISA tools get_study 1.0
PhenoMeNal H2020 Tools ISA tools get_study_json 1.0
PhenoMeNal H2020 Tools ISA tools study_factors 1.0
PhenoMeNal H2020 Tools ISA tools study_factor_values 1.0
PhenoMeNal H2020 Tools ISA tools data_files 1.0
PhenoMeNal H2020 Tools ISA tools factors_summary 1.0
PhenoMeNal H2020 Tools ISA tools mtbls-factors-viz 0.3
PhenoMeNal H2020 Tools ISA tools isatab_validator 1.0
PhenoMeNal H2020 Tools ISA tools isajson_validator 1.0
PhenoMeNal H2020 Tools ISA tools mw2isa 1.0
PhenoMeNal H2020 Tools ISA tools isatab2json 1.0
PhenoMeNal H2020 Tools ISA tools json2isatab 1.0
Clone this wiki locally
You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.
Press h to open a hovercard with more details.