Subject: Re: [bug#30985] [PATCH] gnu: Add delly.

From: Leo Famulari <[email-masked]>
Date: Fri, 30 Mar 2018 10:51:16 -0400

On Thu, Mar 29, 2018 at 03:02:12PM +0200, Roel Janssen wrote:
> Dear Guix,
> 
> I'd like to add Delly.  Note that there's a newer version (0.7.8) out.
> We extensively tested 0.7.7 in our research lab.  Building 0.7.8 failed
> because the patch for unbundling dependencies no longer applies to this
> new version.
> 
> So I'd like to add 0.7.7 first, and do more testing/patching on 0.7.8
> before we update it in Guix.

Okay!

> From b333dd0f027e8dfdcd67bc96ab94f6fc79cf0854 Mon Sep 17 00:00:00 2001
> From: Roel Janssen <[email-masked]>
> Date: Thu, 29 Mar 2018 14:58:15 +0200
> Subject: [PATCH] gnu: Add delly.
> 
> * gnu/packages/bioinformatics.scm (delly): New variable.
> * gnu/packages/patches/delly-use-system-libraries.patch: New file.
> * gnu/local.mk: Include delly-use-system-libraries.patch.

Pushed as fdc306879b388b08be63ead6209473c184daa1e0 with these changes:

> +              (patches
> +               (list
> +                (search-patch "delly-use-system-libraries.patch")))))

I changed this to use search-patches...

> +    (inputs
> +     `(("boost" ,boost)
> +       ("htslib" ,htslib)
> +       ("zlib" ,zlib)
> +       ("bzip2" ,bzip2)))
> +    (native-inputs
> +     `(("python" ,python-2)))
> +    (inputs
> +     `(("boost" ,boost)
> +       ("htslib" ,htslib)
> +       ("zlib" ,zlib)
> +       ("bzip2" ,bzip2)))

... and removed the extra part.