[Bio-packaging] testing out guix

[Pjotr Prins]

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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