README

1 files changed, 23 insertions, 117 deletions

diff --git a/doc/README.org b/doc/README.org
index ecc9b799..adb545f6 100644
--- a/doc/README.org
+++ b/doc/README.org
@@ -2,19 +2,13 @@
 
 * Table of Contents                                                     :TOC:
  - [[#introduction][Introduction]]
- - [[#binary-deployment][Binary deployment]]
-   - [[#install-guix-using-a-tar-ball][Install Guix using a tar ball]]
-   - [[#fix-locale][Fix locale]]
-   - [[#authorize-our-archives][Authorize our archives]]
-   - [[#download-and-install-the-gn2-archive][Download and install the GN2 archive]]
  - [[#source-deployment][Source deployment]]
    - [[#install-guix][Install guix]]
    - [[#checkout-the-git-repositories][Checkout the git repositories]]
-   - [[#run-guix-daemon][Run guix-daemon]]
    - [[#install-gn2][Install GN2]]
    - [[#run-gn2][Run GN2]]
    - [[#run-mysql-server][Run MySQL server]]
-   - [[#other][Other]]
+   - [[#notes][Notes]]
  - [[#source-deployment-and-other-information-on-reproducibility][Source deployment and other information on reproducibility]]
 
 * Introduction
@@ -24,94 +18,9 @@ explain the GeneNetwork deployment system which is based on GNU Guix
 (see also Pjotr's [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]]). The Guix system can be used to install
 GN with all its files and dependencies.
 
-* 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
+The official installation path is via a GNU Guix installation from a
+checked out version of the Guix package tree (this is required for
+reproducibility).
 
 * Source deployment
 
@@ -120,9 +29,14 @@ You can add the last one to your profile
 Deploying from source is also straightforward. Install GNU Guix using
 a binary tar ball as described [[https://github.com/pjotrp/guix-notes][here]].
 
+If it works you should be able to install a package with
+
+: guix package -i hello
+
 ** Checkout the git repositories
 
-Check out the guix and guix-bioinformatics repositories:
+Check out the two relevant guix and guix-bioinformatics git
+repositories:
 
 #+begin_src bash
 cd ~
@@ -133,17 +47,20 @@ git clone --recursive --branch gn-latest https://github.com/genenetwork/guix gui
 cd guix-gn-latest
 #+end_src bash
 
-** Run guix-daemon
+*** Update the path
 
-At this point you may decide to create, install and run a recent
-version of the guix-daemon by compiling the guix repository. Follow
-[[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix][these]] steps carefully.
+Now make sure the guix update path is inline with ours
+
+#+begin_src bash
+mkdir -p ~/.config/guix
+ln -s ~/genenetwork/guix-gn-latest ~/.config/guix/latest
+#+end_src bash
 
 ** Install GN2
 
 #+begin_src bash
-env GUIX_PACKAGE_PATH=../guix-bioinformatics/ \
-  ./pre-inst-env guix package -i genenetwork2
+export GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/
+guix package -i genenetwork2
 #+end_src bash
 
 ** Run GN2
@@ -190,22 +107,11 @@ Set permissions and match password in your settings file below:
 
 : mysql> grant all privileges on db_webqtl_s.* to gn2@"localhost" identified by 'mysql_password';
 
+** Notes
 
-** 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
-
-
+At some point you may decide to create, install and run a recent
+version of the guix-daemon by compiling the guix repository. Follow
+[[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix][these]] steps carefully.
 
 * Source deployment and other information on reproducibility