Updated tutorial for Docker and Singularity for Linux

docs/tutorial_docker.md

@@ -1,10 +1,62 @@
-# Pulling and running FragPipe using Docker
-
-- Install docker by following the [instruction](https://docs.docker.com/desktop/install/mac-install/)
-- Open terminal and pull the docker image: `docker pull fcyucn/fragpipe`
-- (optional) Check the pulled image: `docker image ls -a`
-- Create a Docker container: `docker run -it -v <host directory>:<container directory> fcyucn/fragpipe /bin/bash`. `<host directory>` is the directory in your host machine, and `<container directory>` is the directory you want to map the host directory to container.
-- Then, you have entered the docker, and FragPipe is located in `/fragpipe_bin`
-- Go to `/fragpipe_bin/fragPipe-x.x/fragpipe/bin` directory and execute `./fragpipe --help` in the terminal
+# Running FragPipe using Docker and Singularity
+
+This tutorial covers how to use **Docker** and **Singularity** to run FragPipe. We will run the `fcyucn/fragpipe:<version>` container, first with Docker, then converting it to a Singularity image.
+
+## Prerequisites for Docker and Apptainer (Linux)
+
+Before setting up Docker and Apptainer on Linux, ensure the following:
+
+- **Operating System**: A Linux distribution (e.g., Ubuntu, CentOS, Debian).
+- **Docker Installation**: Install Docker by following the [official guide for Linux](https://docs.docker.com/engine/install/).
+- **Apptainer Installation**: Install Apptainer from the [Apptainer documentation](https://apptainer.org/docs/admin/main/installation.html).
+- **Using Singularity Commands**: Apptainer supports Singularity commands. After installation, you can use `singularity` as the command-line interface (`apptainer` binary serves as `singularity`).
+
+- **User Privileges**: Ensure you have `sudo` privileges for installation.
+
+## Running FragPipe with Docker
+
+1. **Pull and run the Docker container:**
+
+   To run the FragPipe tool directly using Docker, execute:
+
+   ```bash
+   docker run fcyucn/fragpipe:<version> fragPipe-<version>/fragpipe/bin/fragpipe --help
+   ```
+
+   This command will:
+   - Pull the `fcyucn/fragpipe:<version>` image from Docker Hub.
+   - Run the `fragpipe` command inside the container, displaying the help options.
+
+2. **Save the Docker image to a TAR file:**
+
+   To convert the Docker container for use in Singularity, save the Docker image to a tarball:
+
+   ```bash
+   docker save -o fragPipe-<version>.tar fcyucn/fragpipe:<version>
+   ```
+
+   This command will export the Docker image into a file called `fragPipe-<version>.tar`.
+
+## Running FragPipe with Singularity
+
+1. **Convert the Docker image to a Singularity image:**
+
+   Use the exported Docker tarball to create a Singularity image:
+
+   ```bash
+   singularity build fragPipe-<version>.img docker-archive://fragPipe-<version>.tar
+   ```
+
+   This will convert the Docker image into a Singularity image named `fragPipe-<version>.img`.
+
+2. **Run the FragPipe tool with Singularity:**
+
+   Once the Singularity image is built, you can execute the `fragpipe` command with:
+
+   ```bash
+   singularity exec fragPipe-<verison>.img /fragpipe_bin/FragPipe-<version>/fragpipe/bin/fragpipe --help
+   ```
+
+   This command runs the same `fragpipe` tool using the Singularity image, displaying the help options.
 
 Read more: Check [Running FragPipe in command line interface](https://fragpipe.nesvilab.org/docs/tutorial_headless.html) for the instructions running FragPipe in command line interface.