Using the Lifeportal

Katerina Michalickova, Nikolay Vazov

The Research Computing Services, USIT

November 15, 2013

Lifeportal

The Lifeportal at UiO is a portal service to ease the access to high performance computing resources for researchers.

https://lifeportal.uio.no

Topics

• login and user management • Galaxy framework • UiO changes to Galaxy • using Lifeportal

– tools – histories – sharing histories – slurm and Abel – upload a file – run an application

• from Bioportal to Lifeportal • future developments • questions, questions, questions

Login and user/project management

• live demo

Galaxy project Galaxy is "an open, web-based platform for performing accessible, reproducible, and transparent genomic science."

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 experience.

Galaxy framework

Galaxy server

rweb server

database

applications

data

Nekrutenko lab in the Center for Comparative Genomics and Bioinformatics at Penn State and the Taylor lab at Emory University

user authenticat

ion

Galaxy/Lifeportal at UiO

Galaxy server

Apache web server

proxy

USIT database hotel

applications on Abel

data on Abel file system

FEIDE user authentic.

DRMAA

accounting

The Lifeportal – physical configuration

External authentication (FEIDE)

Locally registered users

Apache proxy

Paster (WSGI)

1. accounting DB

2. user DB

node node node

node node node

Abel cluster

SSL connection

Interface between

Galaxy and SLURM – DRMAA

job scheduler - SLURM

VIR

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database hotel

FhGFS partitions mounted on the VM

GOLD

accounting system checking/updating

job accounting module

Using Lifeportal

• live demo

– Apps

– History

– Datasets

– Sharing histories

– Uploading files

– Running an app

– Job params

Bioportal

Phylogeny apps in the Lifeportal

• Live demo

Future developments

• work flows and SLURM

• large files upload

• tuning SLURM parameters to help users

• more tools (emphasis on next generation sequencing)

Resources

• Lifeportal help lifeportal-help@usit.uio.no

• UiO documentation - http://www.uio.no/english/services/it/research/hpc/lifeportal/

• Galaxy project - http://galaxyproject.org/

• Galaxy wiki - http://wiki.galaxyproject.org/

• Galaxy tutorials - http://wiki.galaxyproject.org/Learn

The Lifeportal team

• Developers – Nikolay Vazov (Galaxy framework,user management, user support) – Katerina Michalickova (tool integration, user support) – Georgios Magklaras (Galaxy EMBnet at UiO) – Bjørn-Helge Mevik (Abel job management) – Thierry Toutain (applications on Abel)

• Project leaders – Hans Eide – Gard Thomassen

• Galaxy steering group – Kamran Shalchian-Tabrizi – Eivind Hovig – Hans A. Eide – Nils Christophersen

• Collaborations – ELIXIR Norway