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Galaxy End Users

2012 Galaxy Community Conference (GCC2012), Chicago, Illinois, July 25-27, 2012

A GCC22012Breakout Session

# Participants


These are a merged grouping of Anton's, Dan's, and Jen's notes from the breakout. Please feel free to update, comment, correct or add in anything we didn't have a chance to address during our session.


  • Galaxy Main and CloudMan
  • This group tends to not use Local instances

How Galaxy currently facilitates research

  • Galaxy Main
    • to identify 'vetted' tools
    • to experiment with workflows before committing resources to Cloud instances
  • CloudMan
    • to quickly access an instance with tools/reference data set-up and ready to go
    • for storage (S3)
  • General Comments
    • The 'Big Plus' for end users: Amazon allows Galaxy to be used in highly controlled IT environments.
    • "Galaxy better than commercial software" (the Galaxy Team says "thank-you"!!)
    • Trackster/Sweepster amazed everyone (shout-out to Jeremy!)
    • New end user community to be aware of: Mass spec

What would be most helpful going forward

Better methods to identify 'Vetted' and 'Best Practice' tools

  • Applies to tools on Main, but in particular tools from Tool Shed
  • Community currently relies on Main for this type of information
  • Extends to Libraries & other source Data, Workflows, Visualizations
  • Ideas (some overlap):
    • Best practices as a way to adopt to correct tools
    • A need to explain what is needed for particular analysis goals
    • Tag tools/workflows based on publications, citations, peer-reviewed status
    • DOI would be the ideal tag
    • Methods to evaluate tools in the Tool Shed
    • Tool Shed: Download counts/trends e.g. downloads this week week
    • Tool Shed: Flag bad objects, like craigslist, to alert admin moderator

Data integration between Main and CloudMan

  • S3 bucket attachment
  • Ease transfer of libraries/datasets/histories/workflows/pages/etc (primary objects) between MainCloudMan

Tool integration between Tool Shed and CloudMan

  • Ease installation of tools on cloud instances

ACTION: For all above - Discuss/Prioritize


  • Add a free text "Header tool" that doesn't proliferate/duplicate datasets, or at least keeps to min. Alt actions on form: add line, remove/replace lines. E.g. UCSC custom tracks: track line for bedgraph file, browser line. May be two changes. ACTION: Needs clarification then bitbucket (Dan/Jen)
  • Tools to do file conversions to/from GenomeSpace or was this a "Get Data' tool request? ACTION: Team discuss then bitbucket (Jen)


  • Genome access was hurdle to Local install - Dan mentioned rsync server & auto genome tool. ACTION: Communicate/wiki (Jen/Dan)
  • CloudMan auto-scaling is not working well for long running jobs - e.g. Tophat. ACTION: Team discuss then bitbucket. (Jen)


  • Mailing list → Forum
    • Galaxy-dev 1st. ACTION: Switch now (Dannon/Jen). Maybe add Google Searches (Dave).
    • Galaxy-user 2nd. ACTION: Dual Forum/List ~ 1 year, then transition to forum only. (Dannon/Jen/Dave).
    • Others no change.
  • Trackster .... any data - rna, small genome region, etc. can be used as 'ref genome' with or without sequence. ACTION: Tutorial. (Jeremy/Jen)
  • Multiple versions of tools in UI. ACTION: Tutorial. (Jen)
  • Of interest: CloudMan Costs ~ $900 for 1 flow cell Hi-Seq analysis run. ACTION: Useful info to capture in wiki where users could share usage data? (Dave)

Plan of Action

  • See ACTION items inline above

  • Others to be added


  • Soon!

More to come ...