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-rw-r--r--doc/README.org27
1 files changed, 21 insertions, 6 deletions
diff --git a/doc/README.org b/doc/README.org
index 494e2a70..13f70ad8 100644
--- a/doc/README.org
+++ b/doc/README.org
@@ -13,6 +13,7 @@
- [[#source-deployment-and-other-information-on-reproducibility][Source deployment and other information on reproducibility]]
- [[#trouble-shooting][Trouble shooting]]
- [[#importerror-no-module-named-jinja2][ImportError: No module named jinja2]]
+ - [[#error-can-not-find-directory-homegn2_data][ERROR: can not find directory $HOME/gn2_data]]
* Introduction
@@ -59,12 +60,14 @@ version of the guix-daemon by compiling the guix repository. Follow
** Install GN2
#+begin_src bash
-env GUIX_PACKAGE_PATH=../guix-bioinformatics/ ./pre-inst-env guix package -i genenetwork2 --fallback
+env GUIX_PACKAGE_PATH=../guix-bioinformatics/ ./pre-inst-env \
+ guix package -i genenetwork2 --fallback
#+end_src bash
Note that you can use the genenetwork.org guix substitute caching
server at http://guix.genenetwork.org (which speeds up installs
-significantly because all packages are pre-built).
+significantly because all packages are pre-built). And/or use the Guix
+mirror with option --substitute-urls=http://mirror.guixsd.org
Make a note of the paths with
@@ -147,13 +150,12 @@ R_LIBS_SITE are set) from the information given by guix:
Inside the repository:
-: cd genenetwork2_diet
+: cd genenetwork2
: ./bin/genenetwork2
Will fire up your local repo http://localhost:5003/ using the
-settings in ./etc/default_settings.py
-
-To override settings create your own from a copy of
+settings in ./etc/default_settings.py. These settings may
+not reflect your system. To override settings create your own from a copy of
default_settings.py and pass it into GN2 with
: ./bin/genenetwork2 $HOME/my_settings.py
@@ -162,6 +164,13 @@ and everything *should* work (note the full path to the settings
file). This way we develop against the exact same dependency graph of
software.
+If something is not working, take a hint from the settings file
+that comes in the Guix installation. It sits in something like
+
+: cat ~/.guix-profile/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py
+
+
+
* Source deployment and other information on reproducibility
See the document [[GUIX-Reproducible-from-source.org]].
@@ -184,3 +193,9 @@ On one system:
: export GEM_PATH="$HOME/.guix-profile/lib/ruby/gems/2.2.0"
and perhaps a few more.
+** ERROR: can not find directory $HOME/gn2_data
+
+The default settings file looks in your $HOME/gn2_data. Since these
+files come with a Guix installation you should take a hint from the
+values in the installed version of default_settings.py (see above in
+this document).