Release notes 2017 08
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:
- PhenoMenal Galaxy workflow environment container version v17.05-pheno_cv1.2.99 with >150 tools (based on >50 containers on fixed versions).
- Luigi workflow environment container version v2.6.0_cv0.1.6.
- Jupyter Notebooks container version v387f29b6ca83_cv0.4.9.
The main deployment components of the release are:
- PhenoMeNal Gateway Portal container version v1.0.0_cv0.3.35
- Deployment logic cloud-deploy-kubenow (KubeNow wrap-up for the EBI Portal) version 0.2
- KubeNow version 0.2.1
- Galaxy Helm Chart version 0.3.1
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
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 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
- 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
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
| 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 |
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Funded by the EC Horizon 2020 programme, grant agreement number 654241 |  |
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