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Product backlog
sb10 edited this page Feb 6, 2012
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Here is a list of VRPipe features that need to be implemented, highest priority first.
3. Design a generic (DataSource-like?) DataSink API allowing a Step to output results to an arbitrary database table
3a. Create a new VRPipe Persistent class as an example/default output table
3b. Should be able to output to VRTrack as well
4. Investigate need for iRods DataSource
5. Convert over remaining VertRes pipelines to VRPipe:
5b. Merge-across pipeline
5d. Dindel pipeline
5d.1. Investigate latest Dindel to work out required steps
5f. QC pipeline
5f.1. Genotype checking step
5f.2. QC stats & graphs step (that generically works on genome & exome bams?)
5g. SV calling pipeline
5g.1. Investigate steps needed; avoid use of other pipeline systems
5h. TE calling pipeline
5h.1. Investigate steps needed
5i. RNA-seq & Chip-seq pipelines
5i.1. Investigate steps needed
5j. Design a generic system equivalent of the StoreLane/Path pipelines, but that works on all pipeline outputs and isn't necessarily a "pipeline" a user sets up, but a daemon that acts based on low disc space
5k. Investigate need for import (bam/fasta from file/iRods) pipelines?
6. Cmd-line interface to create new Steps and Pipelines
8. Convert trigger and dispatch scripts into daemons
8a. Trigger daemon should spawn independent daemons for each PipelineSetup
8b. Another monitor daemon should make sure the trigger and dispatch daemons are running, and vice versa
8c. Daemons should send emails out on success and failures
9. Add POD documentation for all code
10. Web interface:
10a. It's own in-built web server daemon
10b. Ajax-tacular
10c. Does all the things the cmd-line interfaces can do, but more pretty
11. Create friendly usage guides and intro here on the wiki
12. Complete DRM independence
12a. Resolve issues with parsing DRM output and resolving back to standard keywords
13. Complete DB independence
13a. Resolve issues with indexing
13b. Resolve issues with column types
13c. Get it working fully on Postgres
14. Write & publish paper