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Repository for Pipe API wrappers for bioinformatics tools #1314

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heuermh opened this issue Dec 12, 2016 · 5 comments
Closed

Repository for Pipe API wrappers for bioinformatics tools #1314

heuermh opened this issue Dec 12, 2016 · 5 comments
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@heuermh
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@heuermh heuermh commented Dec 12, 2016

Thinking about #1313, and also some experiments with the Pipe API https://github.com/heuermh/adam-snpeff and https://github.com/heuermh/adam-dishevelled-bio, I wonder if we should create a new Maven module or new repository for Pipe API wrappers for bioinformatics tools. Such could be popular with external collaborators. A flag for using local binaries vs. call via docker would be useful.

@heuermh heuermh added the discussion label Dec 12, 2016
@heuermh heuermh changed the title Repository for Pipe API wrappers for popular bioinformatics tools Repository for Pipe API wrappers for bioinformatics tools Dec 12, 2016
@fnothaft
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@fnothaft fnothaft commented Dec 12, 2016

+1. I had been thinking "cannoli" would be a good name for this, as cannoli means "little pipe".

@heuermh
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@heuermh heuermh commented Dec 13, 2016

of course, the name is the only hard part

@fnothaft
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@fnothaft fnothaft commented Dec 13, 2016

of course, the name is the only hard part

You ever see the animated Dilbert show? IIRC, they had an entire episode about that.

@heuermh
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@heuermh heuermh commented Jan 9, 2017

Proposal here
https://github.com/heuermh/cannoli

To extend the example to a real tool, imagine Args4J options matching all the tool command line options, those would then populate the string command before calling pipe(string).

I think though that the cannoli API should be more narrow than BDGSparkCommand. The reading and writing from the filesystem in the example probably doesn't need to be there.

@heuermh
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@heuermh heuermh commented Apr 19, 2017

@heuermh heuermh closed this Apr 19, 2017
@heuermh heuermh modified the milestone: 0.23.0 Jul 22, 2017
@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018
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