[debbugs-tracker] bug#30985: closed ([PATCH] gnu: Add delly.)

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Your message dated Fri, 30 Mar 2018 10:51:16 -0400
with message-id <address@hidden>
and subject line Re: [bug#30985] [PATCH] gnu: Add delly.
has caused the debbugs.gnu.org bug report #30985,
regarding [PATCH] gnu: Add delly.
to be marked as done.

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30985: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=30985
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--- Begin Message --- Subject: [PATCH] gnu: Add delly. Date: Thu, 29 Mar 2018 15:02:12 +0200 User-agent: mu4e 1.0; emacs 25.3.1

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.

Thanks for your time!

Kind regards,
Roel Janssen

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--- Begin Message --- Subject: Re: [bug#30985] [PATCH] gnu: Add delly. Date: Fri, 30 Mar 2018 10:51:16 -0400 User-agent: Mutt/1.9.3 (2018-01-21)

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 <address@hidden>
> 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.

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