Introduction to Galaxy at Helix Systems

David Hoover, hooverdm@helix.nih.gov

Helix Systems, CIT/NIH

July 8, 2014


http://galaxy.cit.nih.gov

Quick overview of Galaxy

Dataset

Datatypes and Format

Tags and Annotation

Hidden/Deleted/Purged

Quotas

History

Tools

Versions

Toolshed

https://toolshed.g2.bx.psu.edu/

Workflow

Library

Page

Sharing

Help


Transferring Files

Upload/download file via web

Download file via FTP

Import/export local file

Download from external web server

Import into library


Running Jobs

Color coding: Queued/Running/Paused/Failed/Success

Local versus cluster jobs

Hard-coded resource dependencies

Biowulf users versus Helix-only users


Visualizing Results

Datatype dependency

External web servers and authentication problems

Download and look versus in Galaxy

Trackster/Circster

Genome Browser

IGB/IGV

Ensembl

Others


Organizing Data

Libraries

/data/galaxy/usr


Automating Jobs

Workflows


Troubleshooting

Bug icon

Info icon

Help

Search

Support --> Learn


This document is available as http://helix.nih.gov/talks/galaxy.html
Biowulf home page | Helix Systems | NIH
Last modified: 07 Jul 2014