Notes

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.

Platforms

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 Main ↔ CloudMan

Tool integration between Tool Shed and CloudMan

Ease installation of tools on cloud instances

ACTION: For all above - Discuss/Prioritize

Requests

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)

Issues

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)

Support

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

Solutions

Soon!

More to come ...