Yvan Le Bras
Galaxy-E, a new vision of workflow oriented Biodiversity research?
In ecology, research data analysis is intensively linked to home made, mainly R, scripts executed on personal computers interleaved with ******** Microsoft Excel manipulations. However, in Biodiversity related fields notably, A real huge challenge consists on capturing research analytical processes in a way to facilitate reproducibility of these anlayses by very heterogenous community of users, from scientists to citizens through decision makers and protected area managers. A long time ago, in a no-Galaxy far, far away.... workflows oriented international initiatives have been done based on Taverna in Europe (http://biovel.eu/) or Kepler in US (http://seek.ecoinformatics.org/) and now in Australia (https://portal.coesra.org.au/strudel-web). the GalaxyE project propose to restore a different spark of hope to the fight testing the use of Galaxy to deal with biodiversity related data, tools and workflows.
EWAS tool development / Training / Elixir-CNV community
- my lab activity in galaxy tools development 'EWAS'
- how we utilize galaxy-europe to train our masters and phd students
- update from Elixir-CNV community meeting
Providing Galaxy based bioinformatic environments through cloud technologies
I would like to present ELIXIR-Italy Galaxy instance provier, developed in the framework of the INDIGO-DataCloud project, allowing to fully customize each virtual instance through a user-friendly web interface with tools and reference data, with built-in solution for file system encryption to secure user data.
Marius van den Beek, John Chilton
Travelling with warp-speed, an update on Galaxy workflows
A key feature of Galaxy is the possibility to chain multiple analysis steps together, either ad-hoc via the analysis interface, structured in advance using the Workflow editor or using a combination of both approaches. In this talk we will give a brief overview of the history of workflows in Galaxy and point out recent developments such as subworkflows, versioned workflows, tool upgrades in workflows and workflow tests as well as ongoing efforts to support the common workflow language. We will then point out some difficulties that Galaxy users may run into when using workflows, and analysis scenarios that a cumbersome in the current state-of-the art, and our plans to address these issues in future work. (Research objects, workflow provenance, scheduling errors, workflow progressions, workflow parameters, etc.)
Two customizations in Galaxy
- External Authentication and Authorization. OpenID Connect solution in Apache proxy.
- Resource Allocation and Management in Galaxy. User and project management plug-in