- Plan of Action
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.
How Galaxy currently facilitates research
- to identify 'vetted' tools
- to experiment with workflows before committing resources to Cloud instances
- 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
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
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
More to come ...