From 8677d1b7bd5b32791c440bf0de2fc4c61c98299f Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 21 May 2017 07:21:44 +0000
Subject: Merge from the diet branch.

  * refactored ./bin/genenetwork2 and /etc/default_settings
    - better detection of Guix
    - removed unused parameters, such as GEMMA_RESULT_PATH and TEMP_TRAITS
    - removing some default settings, such as PYLMM_COMMAND
    - rename some settings, such as SQL_URI and LOG_SQL_ALCHEMY
    - added GUIX_JS_PATH for JS modules
  * Added documentation on installing binary GN2
  * Updated Twitter board to latest version in Guix - it had broken
  * Updated many tools in the latest Guix profile
---
 doc/development.org | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 doc/development.org

(limited to 'doc/development.org')

diff --git a/doc/development.org b/doc/development.org
new file mode 100644
index 00000000..bbb6084f
--- /dev/null
+++ b/doc/development.org
@@ -0,0 +1,23 @@
+* Development
+
+After cloning the git source tree you can run the contained GN2 using
+an existing GN2_PROFILE, i.e., use a profile that was create to run a
+binary installation of GN2. This profile may be found by typing
+
+: which genenetwork2
+:   /home/wrk/opt/gn-latest-guix/bin/genenetwork2
+
+An example of running the development version would be
+
+: env GN2_PROFILE=/home/wrk/opt/gn-latest-guix ./bin/genenetwork2
+
+Profiles are stored in /gnu/store, so you may pick one up there
+
+: readlink -f $(dirname $(dirname `which genenetwork2`))
+:   /gnu/store/dvckpaw770b00l6rv4ijql8wrk11iypv-profile
+
+and use that instead.
+
+Note that the genenetwork2 script sets up the environment for running
+the webserver. This includes path to R modules and python modules. These
+are output on startup. To make sure there is no environment pollution you can
-- 
cgit v1.2.3