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From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=)
Subject: Re: [PATCH]: gnu: Add HISAT.
Date: Tue, 10 Feb 2015 00:03:30 +0100
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In-Reply-To: <idjlhk772t8.fsf@bimsb-sys02.mdc-berlin.net> (Ricardo Wurmus's
	message of "Mon, 9 Feb 2015 12:16:19 +0100")
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To: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Cc: Guix-devel <guix-devel@gnu.org>

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> From 305768bfef9bf4bc8d57828e27b8439dedd574bd Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Mon, 9 Feb 2015 12:13:26 +0100
> Subject: [PATCH] gnu: Add HISAT.
>
> * gnu/packages/bioinformatics.scm (hisat): New variable.

Overall looks good to me.  A couple of comments:

> +         (alist-replace
> +          'install
> +          (lambda* (#:key outputs #:allow-other-keys)
> +            (let ((bin (string-append (assoc-ref outputs "out") "/bin/")=
))
> +              (mkdir-p bin)
> +              (for-each (lambda (file)
> +                          (copy-file file (string-append bin file)))
> +                        '("hisat"
> +                          "hisat-build"
> +                          "hisat-build-s"
> +                          "hisat-build-l"
> +                          "hisat-align-s"
> +                          "hisat-align-l"
> +                          "hisat-inspect"
> +                          "hisat-inspect-s"
> +                          "hisat-inspect-l"
> +                          "hisat-build-s-debug"
> +                          "hisat-build-l-debug"
> +                          "hisat-align-s-debug"
> +                          "hisat-align-l-debug"
> +                          "hisat-inspect-s-debug"
> +                          "hisat-inspect-l-debug"))))

If it=E2=80=99s possible to avoid the whole list using =E2=80=98find-files=
=E2=80=99 or
=E2=80=98scandir=E2=80=99, that would be nicer IMO.  If it=E2=80=99s not, t=
hat=E2=80=99s fine.

> +    (license license:gpl3)))

GPLv3-only?

Thanks!

Ludo=E2=80=99.