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#+TITLE: Installing GeneNetwork services with GNU Guix
* Table of Contents :TOC:
- [[#introduction][Introduction]]
- [[#binary-deployment][Binary deployment]]
- [[#from-source-deployment][From source deployment]]
- [[#create-archive][Create archive]]
* Introduction
Large system deployments tend to get very complex. In this document we
explain the GeneNetwork deployment system which is based on GNU Guix
(see Pjotr's [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]]).
* Binary deployment
NYA (will go to README)
* From source deployment
GNU Guix allows for [[https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org][reproducible deployment]] based on a checked out
Guix repository - use gn-stable for that:
#+begin_src sh :lang bash
mkdir genenetwork
cd genenetwork
git checkout https://github.com/genenetwork/guix.git gn-stable-guix
git checkout https://github.com/genenetwork/guix-bioinformatics.git
#+end_src
Next build guix (and run) following the instructions in [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix][guix-notes]].
Once that is done we can add the guix-bioinformatics path with
: env GUIX_PACKAGE_PATH=../guix-bioinformatics command
So
#+begin_src sh :lang bash
#+begin_src sh :lang bash
gn-stable-guix$ env GUIX_PACKAGE_PATH=../guix-bioinformatics ./pre-inst-env guix package -A genenetwork
genenetwork1 1.0-d622c803b out ../guix-bioinformatics/gn/packages/bioinformatics.scm:163:2
genenetwork2 2.0-9e9475053 out ../guix-bioinformatics/gn/packages/bioinformatics.scm:215:2
#+end_src sh :lang bash
Install with
#+begin_src sh :lang bash
gn-stable-guix$ env GUIX_PACKAGE_PATH=../guix-bioinformatics ./pre-inst-env guix package -i genenetwork2
#+end_src sh :lang bash
* Create archive
: env GUIX_PACKAGE_PATH=../../genenetwork/guix-bioinformatics/ ./pre-inst-env guix archive --export -r genenetwork2 > guix_gn2-2.0-9e9475053.nar
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