added additional dropdowns

Author: kyleoconnell-NIH

Submodule_05_Bonus_Notebook.ipynb

@@ -63,9 +63,9 @@
    "outputs": [],
    "source": [
     "#update java\n",
-    "!sudo apt update\n",
-    "!sudo apt-get install default-jdk -y\n",
-    "!java -version"
+    "! sudo apt update\n",
+    "! sudo apt-get install default-jdk -y\n",
+    "! java -version"
    ]
   },
   {
@@ -76,9 +76,47 @@
    "outputs": [],
    "source": [
     "# install mamba and dependencies\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 $HOME/mambaforge\n",
-    "!~/mambaforge/bin/mamba install -c bioconda sra-tools perl-dbd-sqlite perl-dbi -y"
+    "! curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh\n",
+    "! bash Mambaforge-$(uname)-$(uname -m).sh -b -p $HOME/mambaforge"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7df1c464-b102-4e34-8f5f-57dbfc7f43b8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# add mamba to your path\n",
+    "import os\n",
+    "os.environ[\"PATH\"] += os.pathsep + os.environ[\"HOME\"]+\"/mambaforge/bin\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "39bb00de-3481-4cb0-a2fe-098cfdae51a6",
+   "metadata": {},
+   "source": [
+    "Use mamba to install: sra-tools perl-dbd-sqlite perl-dbi from channel bioconda\n",
+    "\n",
+    "<details>\n",
+    "  <summary>Click for help</summary>\n",
+    "\n",
+    "```\n",
+    "mamba install -c bioconda sra-tools perl-dbd-sqlite perl-dbi -y\n",
+    "```\n",
+    "    \n",
+    "</details>"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d1b80a47-89c9-469c-a1f8-9ee3c1817fa7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "! <YOUR COMMAND HERE>"
    ]
   },
   {
@@ -89,9 +127,9 @@
    "outputs": [],
    "source": [
     "#install Nextflow\n",
-    "!curl https://get.nextflow.io | bash\n",
-    "!chmod +x nextflow\n",
-    "!./nextflow self-update"
+    "! curl https://get.nextflow.io | bash\n",
+    "! chmod +x nextflow\n",
+    "! ./nextflow self-update"
    ]
   },
   {
@@ -101,8 +139,22 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Copy the software from the storage bucket\n",
-    "!gsutil -m cp -r gs://nigms-sandbox/nosi-inbremaine-storage/TransPi ./"
+    "# Copy the software from gs://nigms-sandbox/nosi-inbremaine-storage/TransPi\n",
+    "! <YOUR COMMAND HERE>"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "fbb26d8b-21ac-4907-b25a-3bd39b853d1b",
+   "metadata": {},
+   "source": [
+    "<details>\n",
+    "  <summary>Click for help</summary>\n",
+    "\n",
+    "```\n",
+    "gsutil -m cp -r gs://nigms-sandbox/nosi-inbremaine-storage/TransPi ./```\n",
+    "    \n",
+    "</details>"
    ]
   },
   {
@@ -112,8 +164,23 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Copy the data from the storage bucket\n",
-    "!gsutil -m cp -r gs://nigms-sandbox/nosi-inbremaine-storage/resources ./"
+    "# Copy the data from gs://nigms-sandbox/nosi-inbremaine-storage/resources\n",
+    "! <YOUR COMMAND HERE>"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d73e5d6b-9b3f-46e2-9c5c-24713a2ad55c",
+   "metadata": {},
+   "source": [
+    "<details>\n",
+    "  <summary>Click for help</summary>\n",
+    "\n",
+    "```\n",
+    "gsutil -m cp -r gs://nigms-sandbox/nosi-inbremaine-storage/resources ./\n",
+    "```\n",
+    "  \n",
+    "</details>"
    ]
   },
   {
@@ -144,7 +211,7 @@
    },
    "outputs": [],
    "source": [
-    "!ls ./resources/seq2"
+    "! ls ./resources/seq2"
    ]
   },
   {
@@ -165,7 +232,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "9a7bb7e0-f7eb-4166-96a9-b25b0885479c",
    "metadata": {
     "tags": []
@@ -209,8 +276,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!NXF_VER=22.10.1 ./nextflow run ./TransPi/TransPi.nf \\\n",
-    "-profile docker --k 17,25,43 --maxReadLen 50 --all "
+    "! NXF_VER=22.10.1 ./nextflow run \\\n",
+    "    ./TransPi/TransPi.nf \\\n",
+    "    -profile docker \\\n",
+    "    --k 17,25,43 \\\n",
+    "    --maxReadLen 50 \\\n",
+    "    --all "
    ]
   },
   {
@@ -220,14 +291,6 @@
    "source": [
     "With the subsampled reads, the assembly should complete in about 2 hours using a n1-highmem-16 machine."
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "a822011a-4d77-4d99-8124-67ecb8f3dacf",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -238,9 +301,9 @@
    "uri": "gcr.io/deeplearning-platform-release/base-cpu:m113"
   },
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "PySpark (Local)",
    "language": "python",
-   "name": "python3"
+   "name": "local-pyspark"
   },
   "language_info": {
    "codemirror_mode": {
@@ -252,7 +315,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.7.12"
   }
  },
  "nbformat": 4,