Ben Woodcroft <b.woodcr...@uq.edu.au> writes:
>>> + ("python-biopython" ,python2-biopython)))
>> And this looks like it should be a propagated input instead. Have you
>> tried running seqmagick after installing it with this package recipe? I
>> found that Python executables often require either propagated inputs or
>> wrapping in PYTHONPATH to work without runtime errors.
>
> I did, although not well enough to pick up the error you point out.
> Actually I'm a bit confused as to the difference between the input types
> even after reading the manual. Is this a fair summary?
I’m sorry to have confused you here. “biopython” should *not* be a
propagated input here, because “seqmagick” provides an executable, not a
library. I was not aware of the fact that the executables are
automatically wrapped here (although the PYTHONPATH is a little too
broad as you also noted).
> Anyway, it seems as if the package would have worked because a wrapper
> is generated with PYTHONPATH including inputs, propagated-inputs and
> native-inputs. But this seems a bit strange - why would native inputs be
> in the runtime wrapper?
Good question. I think it’s because the wrapping phase just wraps the
scripts in “$out/bin” with whatever the PYTHONPATH variable contains.
It doesn’t construct a minimally sufficient PYTHONPATH. Maybe that’s
worth changing in the python-build-system?
>>> + (synopsis
>>> + "Tools for converting and modifying sequence files from the
>>> command-line")
>> The synopsis is a bit long. You could shave off two words like this:
>>
>> “Command-line tools for converting and modifying sequence files”
>>
>> but that’s not really much better. I’m open to suggestions.
> "Tools for converting and modifying sequence files"
That’s okay.
>>> + (description
>>> + "Bioinformaticians often have to convert sequence files between
>>> formats
>>> +and do little manipulations on them, and it's not worth writing scripts for
>>> +that. Seqmagick is a utility to expose the file format conversion in
>>> +BioPython in a convenient way. Instead of having a big mess of scripts,
>>> there
>>> +is one that takes arguments.")
>>> + (license license:gpl3)))
>>> +
>> I’m not sure if it’s really “GPLv3 only” or “GPLv3 or later” as there
>> are no license headers anywhere. Maybe others could comment what’s the
>> proper declaration here.
> From the readme:
> >|seqmagick| is free software under the GPL v3.
>
> Is that not straightforward enough?
I’m still not sure, but the explicit mention of “v3” is enough for me to
not write “gpl3+” here.
I’ll push your latest patch with minor modifications (undoing the
“propagated-inputs” confusion I caused and moving the synopsis on one
line).
Thanks again!
~~ Ricardo
