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.

TODO: Update below

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 0.3
• KubeNow version 0.3.0
• Galaxy Helm Chart version 0.3.1

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
  • 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

More details available on the PhenoMeNal Galaxy container README file

PhenoMeNal Gateway Portal

The PhenoMeNal Gateway Portal Cerebellin 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, 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

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