On Tue, May 03, 2016 at 07:52:51AM +, Rob Syme wrote:
>Ah. Good point Roel. Until the licencing is resolved, any discussion about
>how to package freebayes is of no practical value. I'll ping Erik about
>the licencing as well :)
To be taken as a serious alternative to GATK, freebay
mus >
> > wrote:
> >
> >>
> >> Hi Rob,
> >>
> >> > A guix-friendly licensed variant caller.
> >> >
> >> > From 78fb1be26ca1a0ac768ce5b98f7fd9f467870b84 Mon Sep 17 00:00:00 2001
> >> > From: Rob Syme
>
;
>> Hi Rob,
>>
>> > A guix-friendly licensed variant caller.
>> >
>> > From 78fb1be26ca1a0ac768ce5b98f7fd9f467870b84 Mon Sep 17 00:00:00 2001
>> > From: Rob Syme
>> > Date: Mon, 2 May 2016 16:46:53 +0800
>> > Subject: [PATCH] gnu: Add freebayes
>&
:00:00 2001
> > From: Rob Syme
> > Date: Mon, 2 May 2016 16:46:53 +0800
> > Subject: [PATCH] gnu: Add freebayes
> >
> > * gnu/packages/bioinformatics.scm (freebayes): New variable.
> >
> > ---
>
> thanks for the patch! I see that freebayes has a couple
Hi Rob,
> A guix-friendly licensed variant caller.
>
> From 78fb1be26ca1a0ac768ce5b98f7fd9f467870b84 Mon Sep 17 00:00:00 2001
> From: Rob Syme
> Date: Mon, 2 May 2016 16:46:53 +0800
> Subject: [PATCH] gnu: Add freebayes
>
> * gnu/packages/bioinformatics.scm (
A guix-friendly licensed variant caller.
>From 78fb1be26ca1a0ac768ce5b98f7fd9f467870b84 Mon Sep 17 00:00:00 2001
From: Rob Syme
Date: Mon, 2 May 2016 16:46:53 +0800
Subject: [PATCH] gnu: Add freebayes
* gnu/packages/bioinformatics.scm (freebayes): New variable.
---
gnu/packa
Leo Famulari writes:
> On Wed, Mar 09, 2016 at 07:53:20AM +0100, Pjotr Prins wrote:
>> On Tue, Mar 08, 2016 at 04:44:13PM +0100, Roel Janssen wrote:
>> > One of the problems with the patch is probably the bulk of dependencies
>> > dragged in (for example, vcflib). They use specific versions so t
rying.
> From 38302e8cac77275694c8793933be414ec26906ec Mon Sep 17 00:00:00 2001
> From: Roel Janssen
> Date: Tue, 8 Mar 2016 16:38:46 +0100
> Subject: [PATCH] gnu: Add freebayes.
> * gnu/packages/bioinformatics.scm (freebayes): New variable.
[...]
> +(define-pub
On Wed, Mar 09, 2016 at 07:53:20AM +0100, Pjotr Prins wrote:
> On Tue, Mar 08, 2016 at 04:44:13PM +0100, Roel Janssen wrote:
> > One of the problems with the patch is probably the bulk of dependencies
> > dragged in (for example, vcflib). They use specific versions so they
> > are tied to this pac
On Tue, Mar 08, 2016 at 04:44:13PM +0100, Roel Janssen wrote:
> One of the problems with the patch is probably the bulk of dependencies
> dragged in (for example, vcflib). They use specific versions so they
> are tied to this package (so that's why I cannot package them separately).
This approach
On Tue, Mar 08, 2016 at 06:55:15PM -0500, Leo Famulari wrote:
> Thanks again for putting such a complicated patch together! We will find
> the best way to add freebayes to the distribution :)
+1. Freebayes is (in my opinion) one of the best variant callers out
there, both for SNPs and somatic (i.e
On Tue, Mar 08, 2016 at 04:44:13PM +0100, Roel Janssen wrote:
Thanks for the patch! This looks like a big one!
[...]
> + (native-inputs
> + `(("cmake" ,cmake)
> + ("htslib" ,htslib)
> + ("zlib" ,zlib)
> + ("python" ,python-2)
> + ("perl" ,perl)
> +
>From 38302e8cac77275694c8793933be414ec26906ec Mon Sep 17 00:00:00 2001
From: Roel Janssen
Date: Tue, 8 Mar 2016 16:38:46 +0100
Subject: [PATCH] gnu: Add freebayes.
* gnu/packages/bioinformatics.scm (freebayes): New variable.
---
gnu/packages/bioinformatics.scm |
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