1 files changed, 98 insertions, 0 deletions
diff --git a/doc/development.org b/doc/development.org
new file mode 100644
index 00000000..e65ccd58
--- /dev/null
+++ b/doc/development.org
@@ -0,0 +1,98 @@
+* Development
+
+** Using GN2_PROFILE
+
+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 $(dirname `which genenetwork2`))
+:   /gnu/store/dvckpaw770b00l6rv4ijql8wrk11iypv-profile
+
+and use that instead.
+
+Note that the genenetwork2 script sets up the environment for running
+the webserver. This includes path to R modules and python modules. These
+are output on startup. To make sure there is no environment pollution you can
+
+** Javascript modules
+
+As of release 2.10-pre4 we Javascript modules are installed in three places:
+
+1. JS_GUIX_PATH: the Guix store - these are Guix pre-packaged modules
+2. The git source tree (./wqflask/wqflask/static/packages/)
+3. JS_GN_PATH: a local directory containing (temporary) development modules
+
+Packages currently in git (2) will move to JS_GUIX_PATH (1) over
+time. This is to keep better track of origin updates. Putting packages
+in git (2) is actively discouraged(!), unless there are GN2 specific
+adaptations to the original Javascript modules.
+
+JS_GN_PATH (3) is for development purposes. By default is is set to
+$HOME/genenetwork/javascript. Say you are working on an updated
+version of a JS module not yet in (1) you can simply check out that
+module in that path and it should show up.
+
+* Python modules
+
+Python modules are automatically found in the Guix profile.
+
+For development purposes it may be useful to try some Python package.
+Obviously this is only a temporary measure and when you decide to
+include the package it should be packaged in [[http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics][our GNU Guix software
+stack]]!
+
+To add packages you need to make sure the correct Python is used (currently
+Python 2.7) to install a package. E.g..
+
+#+BEGIN_SRC sh
+python --version
+  Python 2.7.16
+pip --version
+  pip 18.1 from /usr/lib/python2.7/dist-packages/pip (python 2.7)
+#+END_SRC
+
+You can install a Python package locally with pip, e.g.
+
+#+BEGIN_SRC sh
+pip install hjson
+#+END_SRC
+
+This installed in ~$HOME/.local/lib/python2.7/site-packages~. To add
+the search path for GeneNetwork use the environment variable
+
+#+BEGIN_SRC sh
+export PYTHON_GN_PATH=$HOME/.local/lib/python2.7/site-packages
+#+END_SRC
+
+Now you should be able to do
+
+#+BEGIN_SRC python
+import hjson
+#+END_SRC
+
+In fact you can kick off a Python shell with something like
+
+#+BEGIN_SRC python
+env SERVER_PORT=5013 WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \
+  SQL_URI=mysql://gn2:webqtl@localhost/db_webqtl_s \
+  GN2_PROFILE=~/opt/genenetwork2 \
+  ./bin/genenetwork2 ./etc/default_settings.py -c
+Python 2.7.17 (default, Jan  1 1970, 00:00:01)
+[GCC 7.5.0] on linux2
+Type "help", "copyright", "credits" or "license" for more information.
+>>> import hjson
+#+END_SRC
+
+It should now also work in GN2.
+
+* TODO External tools