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* Binary deployment
Note binary deployment is not working pending a few improvements
to GNU Guix. See source deployment instead.
** Install Guix using a tar ball
GN can be deployed either as a binary tarball or as a GNU Guix
package. First install GNU Guix following the instructions of the
[[https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html#Binary-Installation][binary installation]] using a tar ball from [[https://www.gnu.org/software/guix/download/][here]].
With guix-daemon running you should be able to install the hello
package:
: guix package -i hello
** Fix locale
You may want to
#+begin_src sh :lang bash
export GUIX_LOCPATH=$HOME/.guix-profile/lib/locale
export LC_ALL=en_US.utf8
#+end_src sh :lang bash
** Authorize our archives
Next add our archive key to guix (as root):
#+begin_src scheme
echo "(public-key
(ecc
(curve Ed25519)
(q #E9A95686D8437186302E07C7AB9BF3913F435026C2D389AF27D9C66FD6EBB649#)
)
)
"|guix archive --authorize
#+end_src scheme
if you have trouble finding a suitable guix try
: ls /gnu/store/*guix-*/bin/guix
and you should be able to use this directly, e.g.
: alias guix=/gnu/store/632msbms2yaldfnlrb5lbnlnmn9yjisw-guix-0.9.0/bin/guix
: guix --version
** Download and install the GN2 archive
Find the archive on
http://files.genenetwork.org/software/
download and install with
#+begin_src bash
guix archive --import < genenetwork2-data-hash.nar
#+end_src bash
and you should see a list of packages installing, e.g.
#+begin_src bash
importing path `/gnu/store/l1zs2drn3zdzl5ysjcmhibcpa35p9zfc-python2-mysqlclient-1.3.7'
importing path `/gnu/store/n7kfg4knibvblggy8ci2liscl7vz5wkg-python2-parallel-1.6.4'
importing path `/gnu/store/qvv16qwlq59gp5d07lwbf5n8ndsi3il3-python2-sqlalchemy-1.0.11'
importing path `/gnu/store/qw872mbmr9ir0a9drv9xw9pvjk05ywwy-python2-xlsxwriter-0.8.4'
importing path `/gnu/store/wc112m1xfy3p08v14bdzay2ki2rirdsm-pylmm-gn2-1.0-3c6d1cac8'
importing path `/gnu/store/zfkcy17c2ks3cd9ks14irdabqvmlfpyn-python2-flask-sqlalchemy-2.1'
importing path `/gnu/store/cgcjdiz1qylbc372gc3nda3372ihkpqb-genenetwork2-2.0-a8fcff4'
(etc.)
#+end_src bash
The following packages need to be added and the R path set
: export R_LIBS_SITE="/home/wrk/.guix-profile/site-library/"
: guix package -i /gnu/store/w0dqg9dshq53j8xhcnqgvnvms2s6y5k5-r-wgcna-1.49-425bc170cc0873ddbd414675ac40f6d4d724c7cb
: guix package -i /gnu/store/k60bdlm0v7xic88j2z5c1jb1jvc371mn-r-qtl-1.38-4
You can add the last one to your profile
: guix package -i /gnu/store/cgcjdiz1qylbc372gc3nda3372ihkpqb-genenetwork2-2.0-a8fcff
: export PATH=~/.guix-profile/bin:$PATH
: genenetwork2
or run it directly with
: /gnu/store/cgcjdiz1qylbc372gc3nda3372ihkpqb-genenetwork2-2.0-a8fcff/bin/genenetwork2
** Other
Update guix with a 'guix pull' and make guix visible in the path.
More information exists also in my [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org][guix-notes]].
With guix running you should be able to install python, for example.
: guix package -i python2
This will make python appear in $HOME/.guix-profile/bin/python. Suggested
environment settings can be seen with
: guix package --search-paths
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