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{
"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": {
"scrolled": true
},
"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/api/gemma/version\")\n",
"print(r.json())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Uploading data\n",
"\n",
"Before you perform any computation, you need to ensure you have your data uploaded\n",
"\n",
"TODO"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## K-Computation\n",
"\n",
"Make sure that your metadata file is up to date!\n",
"You need the genofile, traitfile, and snpsfile. You also need a token provided when you first uploaded your metadata file."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Computing K-Values (no loco, no cavariates): \n",
"##### POST /gemma/k-compute/:token\n",
"The end command will look something like:\n",
"\n",
"```\n",
"gemma-wrapper --json -- -debug \\\n",
" -g genotype-file -p traitfile \\\n",
" -a genotypte-snps -gk > input-hash-k-output-filename\"\n",
"```"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Demo\n",
"import requests\n",
"r = requests.post(\"localhost:8080/api/gemma/k-compute/abcde-abcde\")\n",
"print(r.json())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### POST /gemma/k-compute/:chromosomes/:token\n",
"\n",
"Cqmpute K values with chromosomes. The end command will look similar to:\n",
"\n",
"```\n",
" gemma-wrapper --json --loco 1,2,3,4 \\\n",
" -debug -g genotypefile -p traitfile \\\n",
" -a genotype-snps -gk > k_output_filename.json\n",
"```"
]
}
],
"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
}
|
