Re: [PATCH] Add vcflib.

[Ricardo Wurmus]

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?

> +    (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.

~~ Ricardo