updated installation instructions

Author: RamiyapriyaS-NIH

notebooks/GoogleBatch/nextflow/Part2_GBatch_Nextflow.ipynb

@@ -74,7 +74,9 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "cf9e21b4-07d3-4e79-9c94-067b70e78ff6",
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "#make sure you change this name, it needs to be globally unique\n",
@@ -85,7 +87,9 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "e47789f2-e38d-46ec-8750-0a235b0c4337",
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "#will only create the bucket if it doesn't yet exist\n",
@@ -96,7 +100,9 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "5a4ccc7d-b258-410a-85fb-f261fa0dcade",
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "#set versioning on the bucket so it can overwrite old files\n",
@@ -147,7 +153,9 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "2619673e-9645-4460-aa07-323d01bcd9ba",
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "#First install java\n",
@@ -160,7 +168,9 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "c24cb2d9-6260-45fc-a4c0-f55688c43e11",
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "#Specify nexflow version and platfrom\n",
@@ -180,9 +190,26 @@
    "outputs": [],
    "source": [
     "#Install SRAtools to download data\n",
+    "\n",
+    "#Option 1: Using mamba\n",
     "! mamba install -c bioconda -c conda-forge sra-tools==2.11.0 -y"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1242056b-39f3-435d-b0d4-2757c3faa0ff",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#Option 2: Manual Install with wget \n",
+    "\n",
+    "!wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz && \\\n",
+    "tar -xvzf sratoolkit.current-ubuntu64.tar.gz && \\\n",
+    "export PATH=$PATH:$(pwd)/sratoolkit.*-ubuntu64/bin && \\\n",
+    "fasterq-dump --version"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "1bc477a9-7b3f-431e-93b7-50e96809bfc5",
@@ -196,7 +223,9 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "facdbaea-d6ca-4270-9ddc-7c5d042b7373",
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "#set up directory structure\n",
@@ -215,7 +244,9 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "b8ca1c0f-3844-42f8-a9e2-546178a6d961",
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "%%time\n",
@@ -238,7 +269,7 @@
    "outputs": [],
    "source": [
     "%%time\n",
-    "! fasterq-dump -f -e 8 -m 24G SRR067701.sra"
+    "! fasterq-dump -f -e 8 -m 24G SRR067701"
    ]
   },
   {
@@ -398,7 +429,31 @@
    ]
   }
  ],
- "metadata": {},
+ "metadata": {
+  "environment": {
+   "kernel": "conda-base-py",
+   "name": "workbench-notebooks.m129",
+   "type": "gcloud",
+   "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m129"
+  },
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel) (Local)",
+   "language": "python",
+   "name": "conda-base-py"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.16"
+  }
+ },
  "nbformat": 4,
  "nbformat_minor": 5
 }