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Re: [PATCH] Add vcflib.
From: |
Roel Janssen |
Subject: |
Re: [PATCH] Add vcflib. |
Date: |
Tue, 26 Apr 2016 23:50:29 +0200 |
User-agent: |
mu4e 0.9.17; emacs 25.1.50.2 |
Ricardo Wurmus writes:
> Roel Janssen <address@hidden> writes:
>
>> From e75aa388931c92657336c8a15f88b6a0273f5e02 Mon Sep 17 00:00:00 2001
>> From: Roel Janssen <address@hidden>
>> 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
Re: [PATCH] Add vcflib., Ricardo Wurmus, 2016/04/20
Re: [PATCH] Add vcflib., Ricardo Wurmus, 2016/04/20