Re: [PATCH] Add vcflib.

[Ricardo Wurmus <rekado@elephly.net>]

Roel Janssen <roel@gnu.org> writes:

> Ricardo Wurmus writes:
>
>> Roel Janssen <roel@gnu.org> writes:
>>
>>> From e75aa388931c92657336c8a15f88b6a0273f5e02 Mon Sep 17 00:00:00 2001
>>> From: Roel Janssen <roel@gnu.org>
>>> Date: Tue, 22 Mar 2016 15:01:37 +0100
>>> Subject: [PATCH 2/8] gnu: Add smithwaterman.
>>
>>> * gnu/packages/bioinformatics.scm (smithwaterman): New variable.
>>> ---
>>>  gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++
>>>  1 file changed, 31 insertions(+)
>>
>>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
>>> index 6792be9..fa7ba24 100644
>>> --- a/gnu/packages/bioinformatics.scm
>>> +++ b/gnu/packages/bioinformatics.scm
>>> @@ -4830,3 +4830,34 @@ group or two ChIP groups run under different conditions.")
>>>     (description "This is a C++ wrapper around the Tabix project which abstracts
>>>  some of the details of opening and jumping in tabix-indexed files.")
>>>     (license license:expat)))
>>> +
>>> +(define-public smithwaterman
>>> +  (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1"))
>>
>> As there have been new commits since you posted this patch could you add
>> a comment that explains why it should be this particular commit?  Is it
>> because this is the version of the submodule of vcflib?
>
> That is the reason.  I will add a comment in the next patch I send.
>
>>> +    (package
>>> +      (name "smithwaterman")
>>> +      (version (string-append "0-1." (string-take commit 7)))
>>> +      (source (origin
>>> +        (method url-fetch)
>>> +        (uri (string-append "https://github.com/ekg/smithwaterman/archive/"
>>> +                            commit ".tar.gz"))
>>> +        (file-name (string-append name "-" version "-checkout.tar.gz"))
>>> +        (sha256
>>> +         (base32 "1lkxy4xkjn96l70jdbsrlm687jhisgw4il0xr2dm33qwcclzzm3b"))))
>>> +      (build-system gnu-build-system)
>>> +      (arguments
>>> +       `(#:tests? #f ; There are no tests to run.
>>> +         #:phases
>>> +         (modify-phases %standard-phases
>>> +           (delete 'configure) ; There is no configure phase.
>>> +           (replace 'install
>>> +             (lambda* (#:key outputs #:allow-other-keys)
>>> +               (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
>>> +                 (install-file "smithwaterman" bin)))))))
>>> +      (home-page "https://github.com/ekg/smithwaterman")
>>> +      (synopsis "Implementation of the Smith-Waterman algorithm")
>>> +      (description "This package provides an implementation of the Smith-Waterman
>>> +algorithm.")
>>> +      ;; libdisorder is licensed GPLv2.  The parent project (vcflib), of which
>>> +      ;; this program is a submodule, is licensed MIT, which is the same as
>>> +      ;; the Expat license.
>>> +      (license (list license:gpl2 license:expat)))))
>>
>> As far as I can see the license is GPLv2+ as it doesn’t specifically
>> restricts users to version 2.
>>
>> The license of the parent project doesn’t matter in this case, so
>> “(license license:gpl2+)” would seem to be enough.
>
> Where can you see that it's GPLv2+?  I haven't found any licensing
> information other than libdisorder.
>
> I contacted the author about this.  I'm confident it's not an
> intentional nonfree program, but we will have to wait and see.

I see that you’ve opened an issue on Github.  The project now contains a
LICENSE file with the text of the Expat license.  It would be better if
the author clearly stated that the LICENSE file does in fact apply to
the source files in the repository (either in a README or in file
headers).

--
Ricardo

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