boutiques / boutiques-paper Goto Github PK

I'm blown away by the clarity, quality and focus of what is already there.
Bravo!

Note taking, I'll make proper pull requests later:

• I think the Boutiques Github URL should appear in the footnotes of the very first page.
• Add CBRAIN Github URL

It should also mention that they are OSS explicitly.

I think this sentence in the introduction requires a citation:

Meanwhile, virtual container systems such as Docker and Singularity... improve the reproducibility of analyses by defining immutable, reusable execution environments.

Has it been demonstrated (and published) that one can run the same analysis in a container on different machine architectures and achieve the same numerical results? You yourself know very well that if you run the same analyses on different architechtures without using containers, you get different numerical results. Has the test in that paper been run using containers, and were the results reproducible? (I should say that I have been thinking of running that test myself, because that reproducibility is one of the selling points of using containers for processing on our various platforms. I'm not aware that it has yet been shown to be true, but maybe someone has done this.)

I suppose a counter-argument is that the sentence as written is fine and needs no citation because "improve the reproducibility of analyses" does not have to mean "make analyses numerically consistent across architectures". Maybe you still have to use the same architecture to get the same results, but using containers just makes it easier to get a reproduction off the ground. That alone could justify the words "improve the reproducibility of analyses".

features

• resource requirements (cpu, ram) (boutiques/boutiques#63)
• entrypoint support
• docker directory mounting (boutiques/boutiques#96)
• clean examples (boutiques/boutiques#142)
• bosh support for invocation schemas (boutiques/boutiques#141)
• workflows:
  • spark workflows (spark BIDS)
  • MOTEUR workflows (incl MICCAI challenge) @camarasu
  • describe CBRAIN sub-tasking (PSOM)
  • example of a Nipype workflow using boutiques (@ValHayot)
• tests: just focus on coverage.
• API (boutiques/boutiques#150) and documentation.
• publisher to neurolinks
• publish more tools to neurolinks

extra features

• complex object commandlines for SPM (boutiques/boutiques#101, boutiques/boutiques#64)
• brep, a distributed Boutiques repository.

possible additional descriptors or platforms

• nitrc tools (boutiques/boutiques#48)
• nipype tools (boutiques/boutiques#47)
• integration in SPINE

I re-organized a bit the section on ported applications, to add categorical sub-sections. @gkiar, I'd appreciate your input on the classification. @camarasu, I assigned you a few TODOs to add citations of applications ported to VIP.