Add basic gemma documentation on how to use it from gn3

1 files changed, 78 insertions, 0 deletions

diff --git a/docs/gemma.ipynb b/docs/gemma.ipynb
new file mode 100644
index 0000000..b7796e3
--- /dev/null
+++ b/docs/gemma.ipynb
@@ -0,0 +1,78 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Running GEMMA from GN3\n",
+    "\n",
+    "This document outlines how to use gemma from Genenetwork3."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "If you are running gn3 through a development environment, ensure that it is up and running by running the command:\n",
+    "\n",
+    "```sh\n",
+    "env FLASK_APP=\"main.py\" flask run --port 8080\n",
+    "```\n",
+    "\n",
+    "To ensure that things are working, run:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "{'code': 0, 'output': 'gemma-wrapper 0.98.1 (Ruby 2.6.5) by Pjotr Prins 2017,2018\\n'}\n"
+     ]
+    }
+   ],
+   "source": [
+    "import requests\n",
+    "r = requests.get(\"http://127.0.0.1:8080/gemma/version\")\n",
+    "print(r.json())"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "/gnu/store/bvd09gb8ka642jzgxd2lpqlpdp160gn0-python-wrapper-3.8.2/bin/python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}