What bioboxes functions should be demonstrated at the simultaneous talks on November 9th?

bioboxes / rfc

Request for comments on interchangeable bioinformatics containers

http://bioboxes.org

MIT License

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What bioboxes functions should be demonstrated at the simultaneous talks on November 9th? #184

Closed michaelbarton closed 9 years ago

michaelbarton commented 9 years ago

@pbelmann will be presenting bioboxes at the Bio in Docker workshop by @KHP-Informatics. @michaelbarton will be presenting the same day at the UC Davis Docker workshop organised by @ctb. I believe we should coordinate what functionality we are presenting so that it will be consistent.

michaelbarton commented 9 years ago

Here are some initial suggestions:

Merge in the CLI 0.3.0 branch to master, as this contains a lot of new functionality and fixes.
Demonstrate using the CLI to assemble the same sets of reads with different assembly bioboxes.
Demonstate chaining together the signatures and biobox.yaml files by running the assembly validator biobox on the output of several assembler bioboxes.

ctb commented 9 years ago

+1 to all of these!

michaelbarton commented 9 years ago

An additional thought: these recipes will be generally useful all the time and not just at these presentations. I think we should add a recipes section the website for the existing bioboxes. One would be assembly and validation. A second would be binning and assembly. I don't think the signatures match up exactly in the latter case though.

pbelmann commented 9 years ago

@michaelbarton I send you my slides for the workshop.

I want to present:

cli with assemblers and assembly evaluation
Alpha version of the bioboxes gui
continuous evaluation as one use case of bioboxes (nucleotid.es and cami analysis page)

An additional thought: these recipes will be generally useful all the time and not just at these presentations. I think we should add a recipes section the website for the existing bioboxes. One would be assembly and validation. A second would be binning and assembly. I don't think the signatures match up exactly in the latter case though.

Yes we could prepare such a section, but I'm not sure if we should already start present chaining, since as you already mentioned it will not work with all signatures. This is something we still have to figure out.

What do you think?

michaelbarton commented 9 years ago

Demonstrate using the CLI to assemble the same sets of reads with different assembly bioboxes.

Demonstate chaining together the signatures and biobox.yaml files by running the assembly validator biobox on the output of several assembler bioboxes.

I have created a recipe page in bioboxes/bioboxes.org#52 which shows the above functionality. It doesn't however chain containers together using the yaml API but instead used the CLI.

michaelbarton commented 9 years ago

Closing this issue as presentations have been given.