[Bio-packaging] testing out guix

[Pjotr Prins]

Awesome :) That was quick.

For non-core developers submit a patch to the Guix-dev ML. 

  * Making a patch

  A patch can be sent to the mailing list. Use git rebase --interactive
  to merge and squash patches into one. Next use the GNU ChangeLog
  format which is a header with a filewise change description:

    gnu: Add Ruby.
    * gnu/packages/ruby.scm (Ruby): New file.
    * guix/licenses.scm: Add Ruby license information.

  Use git format-patch to send a patch to the mailing list. See also
  the HACKING document in the Guix git repo.

It is a bit elaborate - but usually you get good feedback from the ML.
So that is a win.

Good stuff Ben!

Pj.

On Mon, Jun 08, 2015 at 08:01:22PM +1000, Ben Woodcroft wrote:
> Thanks, figured it out.
> 
> Forgot
>   #:use-module (gnu packages compression)
> 
> At the top. The funky error message was because zlib is a license as
> well as a package.
> 
> win. What's the procedure for contributing this?
> 
> On 08/06/15 19:50, Pjotr Prins wrote:
> >I grepped the package tree.
> >
> >If you check /gnu/packages/scheme.scm you can see
> >
> >    #:use-module (gnu packages zip))
> >
> >that probably does the trick. I found the python.scm particularly
> >enlightning.
> >
> >Pj.
> >
> >On Mon, Jun 08, 2015 at 07:37:06PM +1000, Ben Woodcroft wrote:
> >>Thanks guys,
> >>
> >>I managed to get further now, I think. But not quite there yet.
> >>
> >>ben at u:~/git/OrfM$ GUIX_PACKAGE_PATH=/home/ben/guix/ guix package -i
> >>orfm --no-substitutes
> >>warning: failed to install locale: Invalid argument
> >>guix package: error: ben/packages/my.scm:8:2: package `orfm-0.3.0'
> >>has an invalid input: ("zlib" #<<license> name: "Zlib" uri:
> >>"http://www.gzip.org/zlib/zlib_license.html" comment:
> >>"https://www.gnu.org/licenses/license-list#ZLib">)
> >>
> >>Package file (~/guix/ben/packages/my.scm):
> >>(define-module (ben packages my)
> >>   #:use-module (guix packages)
> >>   #:use-module (guix download)
> >>   #:use-module (guix build-system gnu)
> >>   #:use-module (guix licenses))
> >>
> >>(define-public orfm
> >>   (package
> >>     (name "orfm")
> >>     (version "0.3.0")
> >>     (source (origin
> >>              (method url-fetch)
> >>              (uri (string-append
> >>"file:///home/ben/git/OrfM/orfm-0.3.0.tar.gz"))
> >>              (sha256
> >>               (base32
> >>"18h0mywf87s2dphh0p9mc79li7j44004cz0jg5bmz3pgxi1zshbi"))
> >>              (file-name (string-append name "-" version ".tar.gz"))
> >>             ))
> >>     (build-system gnu-build-system)
> >>     (arguments `(#:configure-flags '("--enable-silent-rules")))
> >>     (inputs `(("zlib" ,zlib)))
> >>     (synopsis "Simple and not slow open reading frame (ORF) caller")
> >>     (description "An ORF caller finds stretches of DNA that when
> >>translated are not interrupted by stop codons.  OrfM finds and
> >>prints these ORFs.")
> >>     (home-page "https://github.com/wwood/OrfM")
> >>     (license lgpl3+)))
> >>
> >>
> >>I installed zlib separately without issue, so doesn't seem to be any
> >>problem there.
> >>
> >>Thanks again,
> >>ben
> >>
> >>On 08/06/15 18:31, Pjotr Prins wrote:
> >>>Adding OSX support will be quite a bit of work, I expect. Better to
> >>>focus on bioinformatics packages for now. We'll get it at some point.
> >>>
> >>>Pj.
> >>>
> >>>On Mon, Jun 08, 2015 at 09:31:57AM +0200, Ricardo Wurmus wrote:
> >>>>Pjotr Prins <pjotr.public66 at thebird.nl> writes:
> >>>>
> >>>>>>* OSX support seems like it would be very pertinent for
> >>>>>>bioinformaticians, does/will guix support?
> >>>>>Nix has OSX support, and there is also little in Guix that can not be
> >>>>>ported to OSX (GNU Guix has multiple targets and even supports the
> >>>>>Hurd!). I expect someone will do it. The project is only gaining
> >>>>>momentum, so once someone competent has the itch to scratch...
> >>>>Actually, I just found out that I *do* have a spare OSX machine lying
> >>>>around here (it was just returned).  I'll need to check with Ludo about
> >>>>how to approach porting and see if I can make time for it.
> >>>>
> >>>>I have *never* used a Mac before, so it'll all be very new to me, but
> >>>>with some help and sufficient hints I might be able to get the bootstrap
> >>>>stuff compiled.
> >>>>
> >>>>>>* Installing from gnu hydra is way slow on the underside of the
> >>>>>>planet, I'm getting DL speeds of 70KB/s. There's no mirrors?
> >>>>>We need to create mirrors. I don't think it is hard to do. Ricardo,
> >>>>>what do you think?
> >>>>I know that it's possible to add machines to the Guix build farm.
> >>>>Alternatively, one could run Hydra on a couple of dedicated machines and
> >>>>offer an additional build farm (maybe limited to x86_64) which could
> >>>>then be authorized.  I don't think "dumb" rsync mirrors are possible at
> >>>>this point, but I'm not the right person to ask, I'm afraid.
> >>>>
> >>>>~~ Ricardo
> >>>>
> 

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