Re: [PATCH]: gnu: Add HISAT.

[ludo@gnu.org (Ludovic Courtès)]

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’s possible to avoid the whole list using ‘find-files’ or
‘scandir’, that would be nicer IMO.  If it’s not, that’s fine.

> +    (license license:gpl3)))

GPLv3-only?

Thanks!

Ludo’.