updated notebook formatting to align with standard format

Author: kyleoconnell-NIH

notebooks/GWAS/GWAS_coat_color.ipynb

@@ -6,17 +6,46 @@
    "metadata": {},
    "source": [
     "# GWAS in the cloud\n",
+    "## Overview\n",
     "We adapted the NIH CFDE tutorial from [here](https://training.nih-cfde.org/en/latest/Bioinformatic-Analyses/GWAS-in-the-cloud/background/) and fit it to a notebook. We have greatly simplified the instructions, so if you need or want more details, look at the full tutorial to find out more.\n",
-    "Most of this notebook is bash, but expects that you are using a Python kernel, until step 3, plotting, you will need to switch your kernel to R."
+    "\n",
+    "Most of this notebook is written in Bash, but expects that you are using a Python kernel, until step 3, plotting where you will need to switch your kernel to R."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3edafe63",
+   "metadata": {},
+   "source": [
+    "## Learning Objectives\n",
+    "The goal is to learn how to execute a GWAS analysis in a cloud environment"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5d7ef396",
+   "metadata": {},
+   "source": [
+    "## Prerequisites\n",
+    "+ You only need access to a Sagemaker notebook environment to run this notebook"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "39ee9668",
+   "metadata": {},
+   "source": [
+    "## Get Started"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "8fbf6304",
    "metadata": {},
    "source": [
-    "## 1. Setup\n",
-    "### Download the data\n",
+    "### Install packages and set up environment\n",
+    "\n",
+    "#### Download the data\n",
     "use %%bash to denote a bash block. You can also use '!' to denote a single bash command within a Python notebook"
    ]
   },
@@ -68,7 +97,31 @@
     "tags": []
    },
    "source": [
-    "## 1. Install dependencies"
+    "### Install dependencies"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9f5032d7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# install mamba\n",
+    "! curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh\n",
+    "! bash Mambaforge-$(uname)-$(uname -m).sh -b -p $HOME/mambaforge"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1a5bd340",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# add to your path\n",
+    "import os\n",
+    "os.environ[\"PATH\"] += os.pathsep + os.environ[\"HOME\"]+\"/mambaforge/bin\""
    ]
   },
   {
@@ -78,6 +131,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# install everything else\n",
     "! mamba install -y -c bioconda plink vcftools"
    ]
   },
@@ -86,7 +140,7 @@
    "id": "3de2fc4c",
    "metadata": {},
    "source": [
-    "## 2. Analyze"
+    "## Analyze"
    ]
   },
   {
@@ -266,7 +320,7 @@
    "id": "1f52e97c",
    "metadata": {},
    "source": [
-    "## 3. Plotting\n",
+    "## Plotting\n",
     "In this tutorial, plotting is done in R, so at this point you can change your kernel to R in the top right. Wait for it to say 'idle' in the bottom left, then continue. You could also plot using Python native packages and maintain the Python notebook kernel."
    ]
   },
@@ -359,6 +413,32 @@
     "\n",
     "The top associated mutation is a nonsense SNP in the gene MC1R known to control pigment production. The MC1R allele encoding yellow coat color contains a single base change (from C to T) at the 916th nucleotide."
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2f6e1ef6",
+   "metadata": {},
+   "source": [
+    "### Conclusion\n",
+    "Here we learned how to run a simple GWAS analysis in the cloud"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "044a04d8",
+   "metadata": {},
+   "source": [
+    "## Clean up\n",
+    "Make sure you shut down this VM, or delete it if you don't plan to use if further.\n",
+    "\n",
+    "You can also [delete the buckets](https://docs.aws.amazon.com/AmazonS3/latest/userguide/delete-bucket.html) if you don't want to pay for the data: `aws s3 rb s3://bucket-name --force`"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c1e7be16",
+   "metadata": {},
+   "source": []
   }
  ],
  "metadata": {