Release notes 2018 02

The 2018-02 release of PhenoMeNal, also known as “Cerebellin”, was released end of February 2018. It represents a major upgrade to the 2017-08 production release. It has a richer set of tools, depends on improved deployment software, includes improved workflows for MS and NMR, and strengthens massively the resilience deployments under high load. As in the previous release, tools and workflows are all tested.

The main user facing components of the release are:

• PhenoMenal Galaxy workflow environment container version v17.09-pheno-lr_cv1.6.175 with >180 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.
• Pachyderm workflow environment v1.6.6.

The main deployment components of the release are:

• PhenoMeNal Gateway Portal container version v2.0.0_cv0.5.66
• Deployment logic cloud-deploy-kubenow (KubeNow wrap-up for the EBI Portal) version 0.3
• KubeNow command line client version 0.3.0 with PhenoMeNal plugin KubeNow-plugin
• Galaxy Helm Chart version 0.3.5

PhenoMeNal Galaxy workflow environment

The Cerebellin release of the PhenoMeNal Galaxy container includes:

• >180 Galaxy tools, based on more than >50 containers, including
  • 5 Tools for data transfer.
  • 3 Tools for metadata creation (ISA related).
  • 5 Tools for metadata exploration (ISA related).
  • 2 Tools for metadata conversion (W4M, ISA).
  • 1 Tool for metadata validation.
  • 12 Tools for NMR data analysis.
  • 8 XCMS modules for MS data analysis
  • 97 OpenMS modules for MS data analysis
  • 8 tools for direct infusion MS data processing (DIMSpy)
  • 26 Tools for MS feature annotation (CAMERA, metfrag, W4M, others)
  • 6 Tools for MS based 13C Fluxomics
  • 12 Tools for Statistical analysis/postprocessing.
• 8 Workflows pre-assembled as example
  • 3 Fluxomics 13C-labeled MS Workflow, with different inputs, with and without final visualization.
  • 1D NMR Workflow
  • LC-MS/MS XCMS-Metfrag Workflow
  • Metabolomics LCMS/MS processing, quantification, annotation, identification and statistics
  • Multi-omics univariate/multivariate analysis Workflow (W4M)
  • W4M Omics generic biosigner feature selection statistics

This PhenoMeNal Galaxy release provides increased reliability for high loads on Kubernetes clusters by setting resources (CPU/RAM) limits for each tool. It includes a new Galaxy composite datatype for the ISA archive standard, and tools that can harness it. Tools are now arranged in an improved thematic layout to facilitate navigation.

More details available on the PhenoMeNal Galaxy container README file and on the CI job built.

PhenoMeNal Gateway Portal

The PhenoMeNal Gateway Portal Cerebellin release includes:

• General reorganisation of the User Interface (UI):
  • user profile indication through a new user menu
  • new CRE menu to rapidly reach the main functionalities to manage CREs
  • new card layout for creating CREs
  • new CRE dashboard which introduces
    • more details for every CRE:
      • creation/destroy time
      • rapid links to the deployed services (Jupyter, Galaxy, Luigi)
    • direct access to deployment logs
  • new page for analyzing deployment logs
• Validation of Cloud Provider credentials (only AWS supported at the moment)
• Fully deployable on Kubernetes through Portal helm charts
• Support CRE deployment on Amazon Web Services (AWS) and Google Cloud Platform (GCP); OpenStack support will be available in short time

KubeNow

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

PhenoMeNal plugin for KubeNow command line tool

Standalone Command Line Client for rapid and customized deployment of PhenoMeNal CRE

• Supports deployment on Amazon Web Services, Google Cloud Platform, Microsoft Azure, OpenStack and KVM.
• Simple usage via Dockerized command line client kn

Cloud deploy KubeNow

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

• Supports deployment on Amazon Web Services, Google Cloud Platform, Microsoft Azure, OpenStack

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
• Handle RBACs
• Automatics Database Schema update