Re: [PATCH] Add vcflib.

[Roel Janssen <roel@gnu.org>]

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.

Kind regards,
Roel Janssen