GNU bug report logs - #30985
[PATCH] gnu: Add delly.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Roel Janssen <roel <at> gnu.org>
Subject: bug#30985: closed (Re: [bug#30985] [PATCH] gnu: Add delly.)
Date: Fri, 30 Mar 2018 14:52:02 +0000

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Your bug report

#30985: [PATCH] gnu: Add delly.

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to 30985 <at> debbugs.gnu.org.

-- 
30985: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=30985
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

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From: Leo Famulari <leo <at> famulari.name>
To: Roel Janssen <roel <at> gnu.org>
Cc: 30985-done <at> debbugs.gnu.org
Subject: Re: [bug#30985] [PATCH] gnu: Add delly.
Date: Fri, 30 Mar 2018 10:51:16 -0400

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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 <roel <at> gnu.org>
> 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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From: Roel Janssen <roel <at> gnu.org>
To: guix-patches <guix-patches <at> gnu.org>
Subject: [PATCH] gnu: Add delly.
Date: Thu, 29 Mar 2018 15:02:12 +0200

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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

[0001-gnu-Add-delly.patch (text/x-patch, attachment)]

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