Cleaning up READMEs - moving stuff to gemtext

2 files changed, 9 insertions, 222 deletions

diff --git a/README.md b/README.md
index 7572cd5f..2e61f0b9 100644
--- a/README.md
+++ b/README.md
@@ -5,8 +5,8 @@ badge](https://ci.genenetwork.org/badge/genenetwork2.svg)](https://ci.genenetwor
 
 # GeneNetwork
 
-This repository contains the current source code for GeneNetwork (GN)
-(https://www.genenetwork.org/ (version 2). GN2 is a Web
+This repository contains the current source code for GeneNetwork (GN2)
+https://genenetwork.org/ (version 2). GN2 is a Web
 2.0-style framework that includes data and computational tools for online genetics and genomic analysis of
 many different populations and many types of molecular, cellular, and physiological data.
 The system is used by scientists and clinicians in the field of precision health care and systems genetics.
@@ -14,218 +14,11 @@ GN and its predecessors have been in operation since Jan 1994, making it one of
 
 ## Install
 
-The recommended installation is with GNU Guix which allows you to
-deploy GN2 and dependencies as a self contained unit on any machine.
-The database can be run separately as well as the source tree (for
-developers).  See the [installation docs](doc/README.org).
-
-## Configuration
-
-GeneNetwork2 comes with a [default configuration file](./etc/default_settings.py)
-which can be used as a starting point.
-
-The recommended way to deal with the configurations is to **copy** this default configuration file to a location outside of the repository, say,
-
-```sh
-.../genenetwork2$ cp etc/default_settings.py "${HOME}/configurations/gn2.py"
-```
-
-then change the appropriate values in the new file. You can then pass in the new
-file as the configuration file when launching the application,
-
-```sh
-.../genenetwork2$ bin/genenetwork "${HOME}/configurations/gn2.py" <command-to-run>
-```
-
-The other option is to override the configurations in `etc/default_settings.py`
-by setting the configuration you want to override as an environment variable e.g.
-to override the `SQL_URI` value, you could do something like:
-
-```sh
-.../genenetwork2$ env SQL_URI="mysql://<user>:<passwd>@<host>:<port>/<db_name>" \
-	bin/genenetwork "${HOME}/configurations/gn2.py" <command-to-run>
-```
-
-replacing the placeholders in the angle brackets with appropriate values.
-
-For a detailed breakdown of the configuration variables and their use, see the
-[configuration documentation](doc/configurations.org)
-
-## Run
-
-Once having installed GN2 it can be run through a browser
-interface
-
-```sh
-genenetwork2
-```
-
-A quick example is
-
-```sh
-env GN2_PROFILE=~/opt/gn-latest SERVER_PORT=5300 \
-    GENENETWORK_FILES=~/data/gn2_data/ \
-    GN_PROXY_URL="http://localhost:8080"\
-    GN3_LOCAL_URL="http://localhost:8081"\
-	SPARQL_ENDPOINT=http://localhost:8892/sparql\
-    ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-dev
-```
-
-For full examples (you may need to set a number of environment
-variables), including running scripts and a Python REPL, also see the
-startup script [./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/bin/genenetwork2).
-
-Also mariadb and redis need to be running, see
-[INSTALL](./doc/README.org).
-
-## Debugging
-
-To run the application under the pdb debugger, you can add the `--with-pdb`
-option when launching the application, for example:
-
-```sh
-env GN2_PROFILE=~/opt/gn-latest SERVER_PORT=5300 \
-    GENENETWORK_FILES=~/data/gn2_data/ \
-    GN_PROXY_URL="http://localhost:8080"\
-    GN3_LOCAL_URL="http://localhost:8081"\
-	SPARQL_ENDPOINT=http://localhost:8892/sparql\
-    ./bin/genenetwork2 ./etc/default_settings.py --with-pdb
-```
-
-**NOTE**: This should only ever be run in development.
-**NOTE 2**: You will probably need to tell pdb to continue at least once before
-the system begins serving the pages.
-
-Now, you can add the `breakpoint()` call wherever you need to debug and the
-terminal where you started the application with `--with-pdb` will allow you to
-issue commands to pdb to debug your application.
-
-## Development
-
-It may be useful to pull in the GN3 python modules locally. For this
-use `GN3_PYTHONPATH` environment that gets injected in
-the ./bin/genenetwork2 startup.
-
-A continuously deployed instance of genenetwork2 is available at
-[https://cd.genenetwork.org/](https://cd.genenetwork.org/). This
-instance is redeployed on every commit provided that the [continuous
-integration tests](https://ci.genenetwork.org/jobs/genenetwork2) pass.
-
-## Testing
-
-To have tests pass, the redis and mariadb instance should be running, because of
-asserts sprinkled in the code base.
-
-Right now, the only tests running in CI are unittests. Please make
-sure the existing unittests are green when submitting a PR.
-
-From the root directory of the repository, you can run the tests with something
-like:
-
-```sh
-env GN_PROFILE=~/opt/gn-latest SERVER_PORT=5300 \
-	SQL_URI=<uri-to-override-the-default> \
-	./bin/genenetwork2 ./etc/default_settings.py \
-	-c -m pytest -vv
-```
-
-In the case where you use the default `etc/default_settings.py` configuration file, you can override any setting as demonstrated with the `SQL_URI` setting in the command above.
-
-In order to avoid having to set up a whole host of settings every time with the `env` command, you could copy the `etc/default_settings.py` file to a new location (outside the repository is best), and pass that to `bin/genenetwork2` instead.
-
-See
-[./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/doc/docker-container.org)
-for more details.
-
-#### Mechanical Rob
-
-We are building 'Mechanical Rob' automated testing using Python
-[requests](https://github.com/genenetwork/genenetwork2/tree/testing/test/requests)
-which can be run with:
-
-```sh
-env GN2_PROFILE=~/opt/gn-latest \
-    ./bin/genenetwork2 \
-    GN_PROXY_URL="http://localhost:8080" \
-    GN3_LOCAL_URL="http://localhost:8081 "\
-    ./etc/default_settings.py -c \
-    ../test/requests/test-website.py -a http://localhost:5003
-```
-
-The GN2_PROFILE is the Guix profile that contains all
-dependencies. The ./bin/genenetwork2 script sets up the environment
-and executes test-website.py in a Python interpreter. The -a switch
-says to run all tests and the URL points to the running GN2 http
-server.
-
-#### Unit tests
-
-To run unittests, first `cd` into the genenetwork2 directory:
-
-```sh
-# You can use the coverage tool to run the tests
-# You could omit the -v which makes the output verbose
-runcmd coverage run -m unittest discover -v
-
-# Alternatively, you could run the unittests using:
-runpython -m unittest discover -v
-
-# To generate a report in wqflask/coverage_html_report/:
-runcmd coverage html
-```
-
-The `runcmd` and `runpython` are shell aliases defined in the following way:
-
-```sh
-alias runpython="env GN2_PROFILE=~/opt/gn-latest TMPDIR=/tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ GN_PROXY_URL="http://localhost:8080" GN3_LOCAL_URL="http://localhost:8081" ./bin/genenetwork2
-
-alias runcmd="time env GN2_PROFILE=~/opt/gn-latest TMPDIR=//tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ GN_PROXY_URL="http://localhost:8080" GN3_LOCAL_URL="http://localhost:8081" ./bin/genenetwork2 ./etc/default_settings.py -cli"
-```
-
-Replace some of the env variables as per your use case.
-
-### Troubleshooting
-
-If the menu does not pop up check your `GN2_BASE_URL`. E.g.
-
-```
-curl http://gn2-pjotr.genenetwork.org/api/v_pre1/gen_dropdown
-```
-
-check the logs. If there is ERROR 1054 (42S22): Unknown column
-'InbredSet.Family' in 'field list' it may be you are trying the small
-database.
-
-### Run Scripts
-
-As part of the profiling effort, some scripts are added to run specific parts of the system under a profiler without running the entire web-server - as such, to run the script, you could do something like:
-
-```
-env HOME=/home/frederick \
-    GN2_PROFILE=~/opt/gn2-latest \
-    GN3_DEV_REPO_PATH=~/genenetwork/genenetwork3 \
-    SQL_URI="mysql://username:password@host-ip:host-port/db_webqtl" \
-	SPARQL_ENDPOINT=http://localhost:8892/sparql\
-    SERVER_PORT=5001 \
-    bin/genenetwork2 ../gn2_settings.py \
-    -cli python3 -m scripts.profile_corrs \
-	../performance_$(date +"%Y%m%dT%H:%M:%S").profile
-```
-
-and you can find the performance metrics at the file specified, in this case, a file starting with `performance_` with the date and time of the run, and ending with `.profile`.
-
-Please replace the environment variables in the sample command above with the appropriate values for your environment.
+The recommended installation is with GNU Guix which allows you to deploy GN2 and dependencies as a self contained unit on any machine. The database can be run separately as well as the source tree (for developers).  See the [installation docs](doc/README.org).
 
 ## Documentation
 
-User documentation can be found
-[here](http://gn2.genenetwork.org/help).  The architecture of the
-software stack is described [here](./doc/Architecture.org).  The
-database schema is (still) shared with GN1 and currently described
-[here](http://www.genenetwork.org/webqtl/main.py?FormID=schemaShowPage). Software
-documentation is being expanded in the
-[source code repository](https://github.com/genenetwork/genenetwork2/tree/master/doc).
-
+User documentation can be found [here](https://genenetwork.org/help).  The architecture of the software stack is described [here](./doc/Architecture.org).  The database schema is (still) shared with GN1 and currently described [here](http://www.genenetwork.org/webqtl/main.py?FormID=schemaShowPage). Software documentation is being expanded in the [source code repository](https://github.com/genenetwork/genenetwork2/tree/master/doc).
 ## Contributing
 
 Issues can be raised through
diff --git a/doc/README.org b/doc/README.org
index e1c6b614..d4dc1027 100644
--- a/doc/README.org
+++ b/doc/README.org
@@ -62,21 +62,16 @@ may support
 
 * Creating a GNU Guix profile
 
-We run a GNU Guix channel with packages at [[https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics][guix-bioinformatics]]. The
-README has instructions for hosting a channel, but typically we use
-the GUIX_PACKAGE_PATH instead. First upgrade to a recent guix with
+We run a GNU Guix channel with packages at [[https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics][guix-bioinformatics]]. The README has instructions for hosting a channel, but typically we use the GUIX_PACKAGE_PATH instead. First upgrade to a recent guix with
 
 : mkdir ~/opt
 : guix pull -p ~/opt/guix-pull
 
-It should upgrade (ignore the locales warnings).  You can optionally
-specify the specific git checkout of guix with
+It should upgrade (ignore the locales warnings).  You can optionally specify the specific git checkout of guix with
 
 : guix pull -p ~/opt/guix-pull --commit=f04883d
 
-which is useful when you ned to roll back to an earlier version
-(sometimes our channel goes out of sync). Next, we install
-GeneNetwork2 with
+which is useful when you need to roll back to an earlier version (sometimes our channel goes out of sync). Next, we install GeneNetwork2 with
 
 : source ~/opt/guix-pull/etc/profile
 : git clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics
@@ -264,10 +259,9 @@ cd $HOME/genotype_files
 
 * GN2 Dependency Graph
 
-Graph of all runtime dependencies as installed by GNU Guix.
+List of all runtime dependencies for GN2 as installed by GNU Guix.
 
-#+ATTR_HTML: :title GN2_graph
-http://biogems.info/contrib/genenetwork/gn2.svg
+https://genenetwork.org/environments/
 
 * Working with the GN2 source code