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

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

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

[Message part 1 (text/plain, inline)]

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)]

Message #10 received at 30985-done <at> debbugs.gnu.org (full text, mbox):

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

[Message part 1 (text/plain, inline)]

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.

[signature.asc (application/pgp-signature, inline)]

Message #13 received at 30985-done <at> debbugs.gnu.org (full text, mbox):

From: Roel Janssen <roel <at> gnu.org>
To: Leo Famulari <leo <at> famulari.name>
Cc: 30985-done <at> debbugs.gnu.org
Subject: Re: [bug#30985] [PATCH] gnu: Add delly.
Date: Fri, 30 Mar 2018 23:45:16 +0200

Leo Famulari <leo <at> famulari.name> writes:

> 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.

Oops.. Thanks for fixing this and pushing!

Kind regards,
Roel Janssen

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