From af7d0bca229f3ebaa80a16d1ce3a2bf1a8abd5df Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 20 Apr 2016 08:37:55 +0000
Subject: [PATCH 023/100] WIP fixing all paths

---
 doc/GUIX-Reproducible-from-source.org | 14 +++++++++++++-
 doc/README.org                        | 23 ++++++++++++++++++++++-
 2 files changed, 35 insertions(+), 2 deletions(-)

(limited to 'doc')

diff --git a/doc/GUIX-Reproducible-from-source.org b/doc/GUIX-Reproducible-from-source.org
index 871156ed..4399ea26 100644
--- a/doc/GUIX-Reproducible-from-source.org
+++ b/doc/GUIX-Reproducible-from-source.org
@@ -4,6 +4,7 @@
  - [[#introduction][Introduction]]
  - [[#binary-deployment][Binary deployment]]
  - [[#from-source-deployment][From source deployment]]
+ - [[#create-archive][Create archive]]
 
 * Introduction
 
@@ -33,10 +34,21 @@ Once that is done we can add the guix-bioinformatics path with
 
 : env GUIX_PACKAGE_PATH=../guix-bioinformatics command
 
-such as 
+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
diff --git a/doc/README.org b/doc/README.org
index 375a5d20..d9730948 100644
--- a/doc/README.org
+++ b/doc/README.org
@@ -3,6 +3,7 @@
 * Table of Contents                                                     :TOC:
  - [[#introduction][Introduction]]
  - [[#binary-deployment-wip][Binary deployment (WIP)]]
+   - [[#install-genenetwork-server][Install genenetwork server]]
    - [[#run-mysql-server][Run MySQL server]]
    - [[#start-the-gn2-server][Start the GN2 server]]
  - [[#source-deployment-and-other-information-on-reproducibility][Source deployment and other information on reproducibility]]
@@ -16,7 +17,27 @@ explain the GeneNetwork deployment system which is based on GNU Guix
 * Binary deployment (WIP)
 
 GN can be deployed either as a binary tarball or as a GNU Guix
-package.
+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]] and, 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
+
+** Install genenetwork server
+
+Fetch the nar file and install it after adding the key with, for
+example
+
+: cat signing-key.pub |.guix-profile/bin/guix archive --authorize
+: guix archive --import < guix_gn2-2.0-9e9475053.nar
 
 ** Run MySQL server
 
-- 
cgit v1.2.3