Updated installing packages in GCP using bash script

Author: hadiparsianNIH

GoogleCloud/01-RNA-Seq/RNA-seq.ipynb

@@ -262,57 +262,34 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "75f2c0da-332b-4b12-8705-897a58fc0e9f",
+   "cell_type": "markdown",
+   "id": "b4788a28",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "# Make installation paths writable so the packages install correctly.\n",
-    "system(\"sudo chmod -R 777 /usr/lib/R/library\", intern=TRUE)\n",
-    "system(\"sudo chmod -R 777 /usr/local/lib/R/site-library\", intern=TRUE)"
+    "Run the following to create a Kernel with all required packaged installed. It will take about 10 minutes to install packages and create a kernel."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4ea2df9e-b6c8-4da4-bbde-4659e28b42f7",
-   "metadata": {},
+   "id": "0a769bb6",
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
    "outputs": [],
    "source": [
-    "# Intall r-base packages\n",
-    "packages <- c(\"hexbin\", \"tidyverse\")\n",
-    "\n",
-    "if (!requireNamespace(\"Biobase\", quietly = TRUE))\n",
-    "  BiocManager::install(\"Biobase\")\n",
-    "install.packages(\"NMF\")\n",
-    "\n",
-    "# Install packages not yet installed\n",
-    "installed_packages <- packages %in% rownames(installed.packages())\n",
-    "if (any(installed_packages == FALSE)) {\n",
-    "  install.packages(packages[!installed_packages])\n",
-    "}"
+    "system('chmod +x install_rna_seq_packages.sh' , intern=TRUE)\n",
+    "system('bash install_rna_seq_packages.sh >> logs.txt' , intern=TRUE) # This creates \"R-RNA-Seq\" kernel"
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "e84050fd-7b86-4d23-8d16-20479e6040e1",
+   "cell_type": "markdown",
+   "id": "bd70d6fe",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "# Install BiocManager if not already installed\n",
-    "if (!require(\"BiocManager\", quietly = TRUE))\n",
-    "  install.packages(\"BiocManager\")\n",
-    "\n",
-    "# Install Bioconductor packages.\n",
-    "packages <- c(\"BSgenome\", \"DESeq2\", \"vsn\", \"genomation\")\n",
-    "\n",
-    "# Install packages not yet installed\n",
-    "installed_packages <- packages %in% rownames(installed.packages())\n",
-    "if (any(installed_packages == FALSE)) {\n",
-    "  BiocManager::install(packages[!installed_packages])\n",
-    "}"
+    "**Important: Choose \"R-RNA-Seq\" kernel for the rest of the notebook.**"
    ]
   },
   {

GoogleCloud/01-RNA-Seq/install_rna_seq_packages.sh

@@ -0,0 +1,33 @@
+#!/bin/bash
+
+conda update -n base -c defaults conda -y
+
+# Create a conda environment
+conda create -n r-package-1 -y
+
+# Consider addressing your conda initialization instead.
+source ~/.bashrc
+
+# Activate the Conda Environment
+conda activate r-package-1
+
+# Install packages
+conda install -c conda-forge -c bioconda bioconductor-deseq2 -y
+
+conda install r-hexbin -y
+
+conda install conda-forge::r-tidyverse -y
+
+conda install bioconda::bioconductor-bsgenome -y
+
+conda install bioconda::bioconductor-vsn -y 
+
+conda install bioconda::bioconductor-genomation -y
+
+conda install bioconda::bioconductor-genomeinfodb -y
+
+R -e 'install.packages(c("NMF","IRkernel"), repos="http://cran.rstudio.com/")'
+
+
+# Install the kernel specification for Jupyter
+R -e 'IRkernel::installspec(name = "R-RNA-Seq", displayname = "R-RNA-Seq")' 

GoogleCloud/02-RRBS/RRBS-downstream.ipynb

@@ -198,41 +198,34 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "c0a10c0c-f13a-40e3-bd08-54529934e720",
+   "cell_type": "markdown",
+   "id": "47daed1e",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "# Intall r-base packages\n",
-    "packages <- c(\"ggplot2\", \"ggforce\", \"tidyverse\")\n",
-    "\n",
-    "# Install packages not yet installed\n",
-    "installed_packages <- packages %in% rownames(installed.packages())\n",
-    "if (any(installed_packages == FALSE)) {\n",
-    "  install.packages(packages[!installed_packages])\n",
-    "}"
+    "Run the following to create a Kernel with all required packaged installed. It will take about 10 minutes to install packages and create a kernel."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f559b564-bf2a-416f-b7cf-71ef61c40d41",
-   "metadata": {},
+   "id": "786a0e20",
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
    "outputs": [],
    "source": [
-    "# Install BiocManager if not already installed\n",
-    "if (!require(\"BiocManager\", quietly = TRUE))\n",
-    "  install.packages(\"BiocManager\")\n",
-    "\n",
-    "## Install Bioconductor packages.\n",
-    "packages <- c(\"methylKit\", \"GenomicRanges\", \"genomation\")\n",
-    "\n",
-    "# Install packages not yet installed\n",
-    "installed_packages <- packages %in% rownames(installed.packages())\n",
-    "if (any(installed_packages == FALSE)) {\n",
-    "  BiocManager::install(packages[!installed_packages])\n",
-    "}"
+    "system('chmod +x install_rrbs_packages.sh' , intern=TRUE)\n",
+    "system('bash install_rrbs_packages.sh >> logs.txt' , intern=TRUE) # This creates \"R-RRBS\" kernel"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6b15565e",
+   "metadata": {},
+   "source": [
+    "**Important: Choose \"R-RRBS\" kernel for the rest of the notebook.**"
    ]
   },
   {

GoogleCloud/02-RRBS/install_rrbs_packages.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+
+# Create a conda environment
+conda create -n r-package-2 r-base=4.2.2 -y
+
+# Consider addressing your conda initialization instead.
+source ~/.bashrc
+
+# Activate the Conda Environment
+conda activate r-package-2
+
+# Install packages
+conda install bioconda::bioconductor-methylkit -y
+
+conda install bioconda::bioconductor-genomicranges -y
+
+conda install bioconda::bioconductor-genomation -y
+
+conda install conda-forge::r-ggforce -y
+
+conda install conda-forge::r-tidyverse -y
+
+R -e 'install.packages(c("IRkernel","ggplot2"), repos="http://cran.rstudio.com/")'
+
+# Install the kernel specification for Jupyter
+R -e 'IRkernel::installspec(name = "R-RRBS", displayname = "R-RRBS")'