[Bio-packaging] testing out guix

[Ben Woodcroft]

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
>>