From mboxrd@z Thu Jan 1 00:00:00 1970 From: Rob Syme Subject: Re: [PATCH] gnu: Add freebayes Date: Tue, 03 May 2016 07:52:51 +0000 Message-ID: References: <87k2jb60w2.fsf@gnu.org> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=001a11c3d09ced5ca70531eb6532 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:41999) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1axV9Z-00023y-Qh for guix-devel@gnu.org; Tue, 03 May 2016 03:54:04 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1axV9N-0006fB-Jf for guix-devel@gnu.org; Tue, 03 May 2016 03:53:52 -0400 In-Reply-To: <87k2jb60w2.fsf@gnu.org> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: Roel Janssen Cc: guix-devel@gnu.org --001a11c3d09ced5ca70531eb6532 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable 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 :) -r P.S. Erik's latest biorxiv preprint is worth a read (A Graph Extension of the Positional Burrows-Wheeler Transform and its Applications): http://biorxiv.org/content/early/2016/05/02/051409 On Tue, 3 May 2016 at 15:46 Roel Janssen wrote: > Hello Rob, > > Actually, at the time I packaged freebayes, I intended to use the > recursive Git fetch, but there was a problem with it in Guix at that > moment. > > So, the clutter in my package should do almost the same as the Git > recursive fetch :). > > There are still some licensing problems with freebayes. First, we need > to get vcflib in Guix, for which the following needs to be resolved: > - fastahack: No free/open source license. > - smithwaterman: No free/open source license. > - tabixpp: No free/open source license. > > For the other dependencies, I sent packages to the list. Some made it > in upstream already (filevercmp), and other are still in review. For > the three packages mentioned above we must first resolve the licensing > issues. > > I sent Erik an e-mail a week ago asking to add licenses to these > projects, and he told me he will look into this soon. Feel free to keep > reminding him to look into this :). > > Kind regards, > Roel Janssen > > > Rob Syme writes: > > > Hi Ricardo > > > > I'm sorry for not checking the list beforehand! Interestingly, we ended > up > > with very different solutions to the problem of including the freebayes > > dependencies. Using the recursive git fetch compiles without issue for = me > > and *seems* to produce sensible results. Perhaps some non-guix packages > are > > bleeding in from my configuration? If so, any verification that it > > works/breaks would be appreciated. If it *does* work, I'd argue that > using > > "(recursive? #t)" is a neater and more upgradable solution to the probl= em > > of the freebayes git submodule problem, as we wouldn't need to update t= he > > hashes and urls for bamtools-src, vcflib-src, tabixpp-src, etc. > > > > On Mon, 2 May 2016 at 23:21 Ricardo Wurmus > > > wrote: > > > >> > >> Hi Rob, > >> > >> > A guix-friendly licensed variant caller. > >> > > >> > From 78fb1be26ca1a0ac768ce5b98f7fd9f467870b84 Mon Sep 17 00:00:00 20= 01 > >> > 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 of git > >> submodules, e.g. for bamtools, intervaltree, and vcflib. I remember > >> Roel was working on this before, trying to untangle all the > >> dependencies. > >> > >> See this discussion here: > >> > >> http://lists.gnu.org/archive/html/guix-devel/2016-03/msg00333.html > >> > >> I don=E2=80=99t see any special treatment of these dependencies in you= r > >> package. Is this not needed? Or does the git checkout include all th= e > >> bundled dependencies? > >> > >> I think we should use one of the release tarballs instead and make sur= e > >> to package the dependencies separately. Maybe you can cooperate with > >> Roel, who has made a lot of progress on this end already. > >> > >> What do you think? > >> > >> ~~ Ricardo > >> > > --001a11c3d09ced5ca70531eb6532 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Ah. Good point Roel. Until the licencing is resolved, any = discussion about how to package freebayes is of no practical value. I'l= l ping Erik about the licencing as well :)
-r

= P.S. Erik's latest biorxiv preprint is worth a read (A Graph Extension = of the Positional Burrows-Wheeler Transform and its Applications):=C2=A0http://biorxiv.org/content/early/2016/05/02/051409

On Tue, 3 Ma= y 2016 at 15:46 Roel Janssen <roel@gnu.o= rg> wrote:
Hello Rob,

Actually, at the time I packaged freebayes, I intended to use the
recursive Git fetch, but there was a problem with it in Guix at that
moment.

So, the clutter in my package should do almost the same as the Git
recursive fetch :).

There are still some licensing problems with freebayes.=C2=A0 First, we nee= d
to get vcflib in Guix, for which the following needs to be resolved:
- fastahack:=C2=A0 No free/open source license.
- smithwaterman: No free/open source license.
- tabixpp: No free/open source license.

For the other dependencies, I sent packages to the list.=C2=A0 Some made it=
in upstream already (filevercmp), and other are still in review.=C2=A0 For<= br> the three packages mentioned above we must first resolve the licensing
issues.

I sent Erik an e-mail a week ago asking to add licenses to these
projects, and he told me he will look into this soon.=C2=A0 Feel free to ke= ep
reminding him to look into this :).

Kind regards,
Roel Janssen


Rob Syme writes:

> Hi Ricardo
>
> I'm sorry for not checking the list beforehand! Interestingly, we = ended up
> with very different solutions to the problem of including the freebaye= s
> dependencies. Using the recursive git fetch compiles without issue for= me
> and *seems* to produce sensible results. Perhaps some non-guix package= s are
> bleeding in from my configuration? If so, any verification that it
> works/breaks would be appreciated. If it *does* work, I'd argue th= at using
> "(recursive? #t)" is a neater and more upgradable solution t= o the problem
> of the freebayes git submodule problem, as we wouldn't need to upd= ate the
> hashes and urls for bamtools-src, vcflib-src, tabixpp-src, etc.
>
> On Mon, 2 May 2016 at 23:21 Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de= >
> wrote:
>
>>
>> Hi Rob,
>>
>> > A guix-friendly licensed variant caller.
>> >
>> > From 78fb1be26ca1a0ac768ce5b98f7fd9f467870b84 Mon Sep 17 00:0= 0:00 2001
>> > From: Rob Syme <rob.syme@gmail.com>
>> > Date: Mon, 2 May 2016 16:46:53 +0800
>> > Subject: [PATCH] gnu: Add freebayes
>> >
>> > * gnu/packages/bioinformatics.scm (freebayes): New variable.<= br> >> >
>> > ---
>>
>> thanks for the patch!=C2=A0 I see that freebayes has a couple of g= it
>> submodules, e.g. for bamtools, intervaltree, and vcflib.=C2=A0 I r= emember
>> Roel was working on this before, trying to untangle all the
>> dependencies.
>>
>> See this discussion here:
>>
>>=C2=A0 =C2=A0 =C2=A0http:/= /lists.gnu.org/archive/html/guix-devel/2016-03/msg00333.html
>>
>> I don=E2=80=99t see any special treatment of these dependencies in= your
>> package.=C2=A0 Is this not needed?=C2=A0 Or does the git checkout = include all the
>> bundled dependencies?
>>
>> I think we should use one of the release tarballs instead and make= sure
>> to package the dependencies separately.=C2=A0 Maybe you can cooper= ate with
>> Roel, who has made a lot of progress on this end already.
>>
>> What do you think?
>>
>> ~~ Ricardo
>>

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