Getting biopython tools into the TS

bgruening / galaxytools

:microscope::books: Galaxy Tool wrappers

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Getting biopython tools into the TS #132

Open bgruening opened 9 years ago

bgruening commented 9 years ago

@peterjc @erasche (because your are both heavily involved in genome annotation). We are running a genome annotation workshop in the end of this month here and I would like to include our biopython tools from: https://github.com/bgruening/galaxytools/tree/master/tools/biopython into the TS before. I started this many years back but never put them into the TS.

I'm planning to add

[ ] tests
[ ] tool dependencies
[ ] citations
[ ] macros

What is your opinion on one biopython tool repository vs. many single repositories? Should I put everything in one github folder but trying the planemo demultiplexing feature to create several TS repositories? Are these tools good enough? Should I skip a few (e.g. translate?), because they are already in EMBOSS? General comments?

hexylena commented 9 years ago

Unless you're test-data then I'd say it's a logical separate for single repositories with perhaps a suite linking them. If they're
https://github.com/bgruening/galaxytools/blob/master/tools/biopython/codon_count.py#L26 might want to switch to english errors ;)
Are most of these tools not already part of emboss? I feel like I've seen a translate, a reverse+comp, various GC distribution tools elsewhere?

hexylena commented 9 years ago

@jmchilton we're still hoping to get biopython as a dependency in Galaxy, yes?

bgruening commented 9 years ago

@erasche translate and reverse+comp probably, I need to look it up. But all the converters (which aren't real Galaxy converter, because of multiple inputs) are not included and I need them :)

peterjc commented 9 years ago

For now there are Biopython packages in the Tool Shed which this can point at.

peterjc commented 9 years ago

If would also favour separate TS repositories with suite entry to make getting the whole set easier.

jmchilton commented 9 years ago

@erasche absolutely would still like to make biopython available for datatypes. In general though tools should not rely on Galaxy eggs for dependencies - so the tool shed package for biopython is still the way to go here I think.

hexylena commented 9 years ago

@jmchilton ok! (This ping was more for the converters since there are a couple dozen in that directory)