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Diffstat (limited to 'doc')
| -rw-r--r-- | doc/README.org | 27 |
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). |