[Bio-packaging] testing out guix

[Pjotr Prins]

Hi Ben,

If posting a patch is too much I suppose someone could do it for you.
We could create a bioinformatics git repo to merge against. Would that
be useful?

Pj.

On Mon, Jun 08, 2015 at 04:05:50PM +1000, Ben Woodcroft wrote:
> Hey,
> 
> Based on discussions from this list I thought I might give it a
> spin, but ran into a few problems (on 0.8.2). Specifically, I was
> unable to get a "hello world" package of my own making to work,
> presumably because of my own ignorance. Maybe someone can help me
> out. Seeing as package files seem quite straightforward to write,
> I'm hoping it won't be too much effort to write one for each piece
> of software that we publish.
> 
> I tried to follow the instructions at
> https://www.gnu.org/software/guix/manual/guix.html#Defining-Packages
> 
> but it is unclear what to do with the 'recipe' once created. Where
> do I put it? What is a good name for a recipe file? How do I
> test/install it? It would be great to have a blog post that steps
> through the process of creating a new package to follow.
> 
> 
> Some other problems/notes - Apologies for being wide-ranging.
> * OSX support seems like it would be very pertinent for
> bioinformaticians, does/will guix support?
> * 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?
> * For some reason my per-user profile is a broken soft-link:
> 
> $ ls -lh ~/.guix-profile
> lrwxrwxrwx 1 ben ben 44 Jun  8 13:40 /home/ben/.guix-profile ->
> /var/guix/profiles/per-user/ben/guix-profile
> $ ls -A /var/guix/profiles/per-user/ben/
> $
> 
> 
> For completism's sake, here is my (quite buggy I'm sure) recipe, and
> log of my install of guix.
> 
> (define-module (gnu packages orfm)
>   #: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 "0.2.0")
>     (source (origin
>              (method url-fetch)
>              (uri (string-append
> https://github.com/wwood/OrfM/archive/v" version ".tar.gz))
>              (sha256
>               (base32 "7141fd43ecef8e5f5779127c460020449e48d361355d00e16d421fe4b8af00a2"))))
>     (build-system gnu-build-system)
>     (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+)))
> 
> 
> ben at u:~/bioinfo$ wget ftp://alpha.gnu.org/gnu/guix/guix-binary-0.8.2.x86_64-linux.tar.xz
> ...
> 
> ben at u:/$ sudo tar xf ~/bioinfo/guix-binary-0.8.2.x86_64-linux.tar.xz
> [sudo] password for ben:
> 
> ben at u:/gnu$ sudo -i
> root at u:~# groupadd --system guix-builder
> root at u:~# for i in `seq 1 10`;
> >  do
> >    useradd -g guix-builder -G guix-builder           \
> >            -d /var/empty -s `which nologin`          \
> >            -c "Guix build user $i" --system          \
> >            guix-builder$i;
> >  done
> root at u:~# /root/.guix-profile/bin/guix-daemon --build-users-group=guix-builder
> ^C
> root at u:~# /root/.guix-profile/bin/guix-daemon --build-users-group=guix-builder &
> [1] 1029
> root at u:~# cd /usr/local/bin
> root at u:/usr/local/bin# ln -s /root/.guix-profile/bin/guix
> root at u:/usr/local/bin# guix archive --authorize < /root/.guix-profile/share/guix/hydra.gnu.org.pub
> warning: failed to install locale: Invalid argument
> root at u:/usr/local/bin# fg
> /root/.guix-profile/bin/guix-daemon --build-users-group=guix-builder	(wd: ~)
> ^C
> root at u:/usr/local/bin# /root/.guix-profile/bin/guix-daemon --build-users-group=guix-builder &
> [1] 1186
> ben at u:~/git/OrfM$ guix package -i emacs
> warning: failed to install locale: Invalid argument
> The following package will be installed:
>    emacs	24.5	/gnu/store/7l7nvb8mm22cij39fr2mw40z4fqmya3q-emacs-24.5
> 
> substitute: warning: failed to install locale: Invalid argument
> substitute: updating list of substitutes from 'http://hydra.gnu.org'... 100.0%
> The following derivations will be built:
>    /gnu/store/a34r3s8zgg1br29j97dhvf32p9bjr514-profile.drv
>    /gnu/store/sa3li6wf2yl2h8bp2h0f7hyh0bdnrs8c-ca-certificate-bundle.drv
>    /gnu/store/8x40mds6p2hmqqv7j25c4d513h177zcz-info-dir.drv
> The following files will be downloaded:
>    /gnu/store/cnqmkmj40jmssnx6fkf9n0n3bqj5x426-guile-2.0.11
>    /gnu/store/kbf46vds6f7lp723xn62kgdaxmwc1jvi-module-import-compiled
>    /gnu/store/x41ghgfg03z6mv616jmfihqijxdckvyx-glibc-utf8-locales-2.21
>    /gnu/store/7l7nvb8mm22cij39fr2mw40z4fqmya3q-emacs-24.5
> ...
> 
> 
> 
> 
> Thanks,
> ben
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