Documentation added to run shinyscreen inside docker container

Docker_Documentation/Shinyscreen_Docker.Rmd

+---
+title: "shinyscreen Docker Documentation"
+author: "Anjana Elapavalore"
+date: '`r Sys.Date()`'
+output: pdf_document
+---
+
+The objective of this documentation is to provide a detailed procedure for running the shinyScreen application within a Docker container. shinyScreen is a web-based tool developed for visualizing and analyzing high-throughput screening data using Shiny, a web application framework for R. Docker is employed to containerize the application, ensuring reproducibility and simplifying the deployment process by packaging the application with all its dependencies.
+
+This document provides step-by-step instructions on how to install Docker, pull the ShinyScreen Docker image, and run the application.
+
+## Prerequisites
+
+Before proceeding, the following prerequisites must be met:
+
+- Docker Desktop must be installed and properly configured on the system.
+- Sufficient system resources, including at least 4 GB of RAM, are recommended for optimal performance.
+
+## Step 1: Install Docker Desktop on Windows
+
+If Docker Desktop is not already installed on your system, follow these steps to set it up:
+
+1. **Download Docker Desktop**:
+   - Visit the [Docker Desktop for Windows](https://docs.docker.com/desktop/install/windows-install/) download page and download the installer.
+   
+2. **Install Docker Desktop**:
+   - Run the downloaded installer.
+   - Follow the installation prompts, and make sure the option to "Use the WSL 2-based engine" is selected during setup (if available).
+   
+3. **Verify Docker Installation**:
+   - After installation, launch Docker Desktop.
+   - Ensure Docker is running by checking the Docker icon in the system tray (it should be active).
+   - Open a command prompt (CMD) or PowerShell and type the following command to check the Docker version:
+
+```bash
+
+docker --version
+
+```
+
+This should return the installed Docker version.
+
+## Step 2: Search for the ShinyScreen Docker Image in Docker Desktop
+
+Docker Desktop provides a graphical interface to search for Docker images. To search and pull the **shinyScreen** Docker image:
+
+1. **Open Docker Desktop**:
+   - Launch Docker Desktop from the Windows Start menu or by clicking the Docker icon in the system tray.
+
+2. **Search for the ShinyScreen Image**:
+   - In Docker Desktop, navigate to the **search** tab as shown in the image below.
+   
+```{r, echo=FALSE, out.width="70%"}
+knitr::include_graphics("images/searchtab.png")
+
+```
+
+3. **Pull the Image**:
+   - Click on the **Pull** button next to the desired ShinyScreen image. This will download the image to your local system.
+
+You can monitor the download progress in Docker Desktop’s **Images** tab.
+
+## Step 3: Run the ShinyScreen Docker Container
+
+Once the ShinyScreen image has been pulled successfully, the next step is to run the container. This can be done directly from Docker Desktop or via the command line:
+
+### Running the Container via Docker Desktop:
+
+1. **Navigate to the Images Tab**:
+   - In Docker Desktop, go to the **Images** tab where your downloaded ShinyScreen image will be listed.
+
+2. **Launch the Container**:
+   - Click the **Run** button next to the ShinyScreen image.
+   - In the pop-up dialog, ensure that port `3838` is exposed. To do this, add the following port configuration in the **Optional Settings**:
+     
+```
+Host Port: 3838
+Container Port: 3838
+
+```
+3. **To create the volume mounts**:
+
+  - To share files between the host and the container, you can use Docker’s volume mounting          feature.
+  
+### local Directory Structure
+
+Before launching the Docker container, the following directory structure should be set up on your local system. These directories will be mounted to specific locations inside the container, enabling the application to access the required input data and store the output files.
+
+### Root Directory
+
+The **root directory** is the top-level folder where the entire project is organized. This root directory will contain the following subdirectories:
+1. **Project Directory**
+2. **Data Directory**
+3. **MetFrag Databases Directory**
+
+Below is an overview of each subdirectory and its purpose.
+
+### Project Directory
+
+The **Project Directory** should initially contain only the **compound list** file, which is an essential input for the ShinyScreen application.
+
+After the application runs, this directory will also store various output files generated during the analysis.
+
+### Data Directory
+
+The **Data Directory** should contain only the **mzML files**. These files serve as the primary data input for the ShinyScreen application and represent mass spectrometry data in mzML format.
+
+### MetFrag Databases Directory
+
+The **MetFrag Databases Directory** must include the latest **PubChemLite_Exposomics.csv** file, which will be used by the ShinyScreen application for MetFrag analysis.
+
+
+### Configure Volume Mounts in Docker Desktop
+
+Now that the local directories are set up, you can configure **volume mounts** in Docker Desktop to map these local directories to the corresponding paths inside the Docker container.
+
+For the volume mounts, each directory on the host machine (local system) will be mapped to a specific location within the Docker container, allowing the application to access the input data and save output files.
+
+In the **Optional Settings** pop-up window, you will configure the following **three volume mounts** (Please refer to the table and image below):
+
+   - **Local Directory on Windows**: 
+     - This is the folder on your local machine where the data will reside.
+   - **Container Directory**: 
+     - This is the path inside the Docker container where the files will be mounted.
+
+
+| Local Directory (Host)         | Container Directory (Mount)            | Description                     |
+| ------------------------------ | -------------------------------------- | ------------------------------- |
+| `C:\path\to\rootdirectory`           | `/home/ssuser/projects`                | Directory for project files.     |
+| `C:\path\to\rootdirectory`       | `/home/ssuser/top_data_dir`            | Directory for top-level data.    |
+| `C:\path\to\metfrag_dbs`        | `/home/ssuser/metfrag_dbs`             | Directory for MetFrag databases. |
+
+```{r, echo=FALSE, out.width="70%"}
+knitr::include_graphics("images/runtab.png")
+
+```
+
+By setting up the volume mounts, any changes made to files in the mapped directories on the host machine will automatically reflect inside the container.
+
+Once the **port** and **volume configurations** are confirmed, click **Run** to start the container. The ShinyScreen application will now be running inside the container.
+
+Now click on the port mapping to access the application in the web browser
+
+```{r, echo=FALSE, out.width="85%"}
+knitr::include_graphics("images/containertab.png")
+
+```
+
+
+