Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience. AGINFRA+ VREs include access to a Galaxy deployment where researchers can make use of the usual Galaxy features and also interact with the DataMiner platform to run the available algorithms. The webinar introduced Galaxy, the available deployment for AGINFRA+ VREs and the DataMiner integration. Τhe webinar was described by Enol Fernández from EGI Advanced Computing Services for Research.

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AGINFRA PLUS - Accelerating user-driven e-infrastructure innovation
in Food & Agriculture has received funding from the European Union’s
Horizon 2020 research and innovation programme under grant
agreement No 731001.
Galaxy for AGINFRA+ VREs
Online webinar | January 2019
Enol Fernández
EGI Foundation

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Webinar is being recorded!
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Demonstrate how scientific communities working
on agriculture and food topics may carry out rapid
and intuitive development and deployment of
innovative applications and workflows, powered
by open e-infrastructures.
Strengthen and illustrate the value and potential
of AGINFRA+ as a virtual research environment
for the domain of agriculture and food.
The AGINFRA+ Vision
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Enol Fernández
 Cloud Architect @ EGI Foundation
 Working since 2003 on computing e-infrastructures
(grid, cloud)
 Support to user communities
 EGI Cloud Federation Coordinator
 Development of new services for EGI
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/usr/bin/whoami

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Galaxy
Galaxy integration in AGINFRA+
Demo
Q&A
Outline
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Galaxy
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Web-based platform for computational
biomedical research (analysis and data
integration)
Open source, community driven software that
makes integrating your biomed tools simple
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Galaxy is "an open, web-based platform for performing
accessible, reproducible, and transparent genomic
science.”
Accessibility
 Users without programming experience can easily upload/retrieve
data, run complex tools and workflows, and visualize data
Reproducibility
 Galaxy captures information so that any user can understand and
repeat a complete computational analysis
Transparency
 Users can share or publish their analyses (histories, workflows,
visualizations)
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Galaxy: core values

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Galaxy interface
Toolbar HistoryMain

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Tools manipulate and transform your data
Each tool is defined by:
 input datasets, parameters, commands, and outputs
 help, tests, citations, dependency requirements
New versions can be installed without removing
old ones to ensure reproducibility
Galaxy Tool Shed: application store with +1000
tolos ready to be used
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Tools

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Every action and dataset is tracked on the history
 Datasets produced by tools
 Operations performed on data
Includes:
 name, format, size, creation time, datatype-specific
metadata
 tool id, version, inputs, parameters
 standard output (stdout) and error (stderr)
 state (waiting, running, success, failed)
 hidden, deleted, purged
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History

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History management

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Series of tools and dataset actions that run in
sequence as a batch operation
 From history, from scratch with visual editor or import
Allow to re-run the same analysis on different input
data sets
 Change parameters before re-running a similar analysis
Workflows can be annotated, viewed, shared,
published, and imported - just like other Galaxy
objects.
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Workflows

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Workflow editor
Image taken from https://mgescan.readthedocs.io/en/latest/workflow.html

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Galaxy on AGINFRA+
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Workflow design and execution technologies are
key for the research activities of the use cases
Two platforms selected:
 KNIME
 Galaxy
Integration with AGINFRA+:
 Access the workflow platforms within the VRE
 Access other VRE tools form the workflow platforms
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Workflows on AGINFRA+

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Custom wsgi filter for Galaxy
 Leverages support for external authentication in
Galaxy
 Exposes REMOTE_USER with information from
D4Science
 Stores the D4Science token to further interaction with
the VRE
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Authentication

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DataMiner and Galaxy
Periodic synchronisation of
DataMiner as tools in Galaxy
Execution using WPS calls to
Dataminer
 With user token
 Use DataMiner algorithm as
any other Galaxy tool

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Some limitations
Input files must be provided as URLs
 No easy way to discover the files from the Galaxy
interface
Output is stored as HTML with pointers to the
actual outputs
 Can still be easily converted to other more friendly
format as needed
 A csv extractor provided to facilitate that case, more
can be created.

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Kubernetes Cluster (EGI Cloud Container Compute)
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Deployment
SSL Certificate
Kubernetes
Ingress
AuthN
filter
WPS calls

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DEMO!
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Galaxy available now for AGINFRA+ VREs
 Go and test!
Start collecting your feedback:
 Add new tools as needed by use cases
 Improve the integration with DataMiner (input and
output files)
 Expand deployment as usage grows
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Next steps

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Galaxy: https://galaxyproject.org/
Galaxy Tutorials: https://galaxyproject.org/learn/
Galaxy training:
https://galaxyproject.github.io/training-material/
Galaxy ToolShed: https://toolshed.g2.bx.psu.edu/
DataMiner: https://wiki.gcube-
system.org/gcube/DataMiner_Manager
AGINFRA+ VREs: https://aginfra.d4science.org/
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Reference

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CONSORTIUM
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Thanks!
Questions?
@enolfc
https://linkedin.com/in/enolfc/
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