[Bio-packaging] testing out guix

[Ben Woodcroft]

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
>>>>