# Get Started with BioContainers using Rafay

In this step-by-step guide, the Bioinformatics data scientist will use Rafay's end user portal to launch a **well resourced** remote VM and run a series of BioContainers with Docker.

---

## Prerequisites

- Access to Rafay's end user self-service portal (i.e. Developer Hub)
- An SSH client (e.g., PuTTY on Windows, Terminal on macOS/Linux)
- An SSH Public Key

---

## Step 1: Launch a Remote VM

This step covers the creation and deployment of the remote VM using Rafay's Developer Hub. Watch a brief video of the end user experience below.

Run BioContainers with Docker on a Remote VM \| Rafay Platform - YouTube

[Run BioContainers with Docker on a Remote VM \| Rafay Platform](https://www.youtube.com/watch?v=LVxt3voei6w)

1. **Navigate to Compute Instances:**  
   - Log in to your Developer Hub.  
   - On the dashboard, find and click on "Compute Instances."
2. **Create a New Compute Instance:**  
   - Click the "New Compute Instance" button.

3. **Select a Compute Profile:**  
   - From the "Compute Profile" dropdown, choose a profile that meets your needs, for example, "VMAAS - Large (4 GPU)" if you require significant GPU resources.
4. **Configure Instance Details:**  
   - Fill in the required details for your new VM:  
     - **Name:** Enter a descriptive name (e.g., `demo-vm-biocontainers`).  
     - **Compute Profile:** Confirm your selected profile (e.g., `vmaas`).  
     - **Workspace:** Select your desired workspace (e.g., `demo`).  
     - **CPUs:** Specify the number of CPUs (e.g., `44 vCPUs`).  
     - **Disk Storage (GB):** Set the disk size (e.g., `100 GB`).  
     - **GPUs:** Specify the number of GPUs (e.g., `1 GPU`).  
     - **Memory (MB):** Set the memory allocation (e.g., `130 GB`).  
     - **Image:** Choose the operating system image (e.g., `Ubuntu 24.04`).  
   - Note that the user can request substantial compute, memory, GPU, and storage resources that are not possible on end user laptops.

5. **Add SSH Public Key:**  
   - Paste your SSH Public Key into the designated field.  
   - Note that this SSH key will be used to securely connect to the remote VM.
6. **Create and Publish the Instance:**  
   - Click the "Create" or "Publish" button to initiate the VM deployment.
7. **Monitor Deployment Status:**  
   - Observe the deployment status. It will typically transition through "Pending," "In Progress," and finally to "Success."  
   - Once successful, note down the **IP Address** and **Username** displayed for your VM. These are crucial for connecting via SSH.

---

## Step 2: Launch a BioContainer Using Docker on the Remote VM

This step details how to connect to your VM and run Docker commands to manage and execute BioContainers.

1. **Connect to Your Remote VM via SSH:**
   - Open your SSH client (e.g., Terminal on macOS/Linux, PuTTY on Windows).  
   - Use the `ssh` command with the Username and IP Address you noted earlier:
   ```
   ssh [Username]@[IP_Address]
   # Example: ssh ubuntu@192.0.2.1
   ```
   - If prompted, accept the authenticity of the host.
2. **Verify Docker Installation:**
   - Once connected, ensure Docker is correctly installed by checking its version:
   ```
   docker --version
   ```
   - You should see output similar to `Docker version 24.0.5, build 24.0.5-0ubuntu1~22.04.1`.
3. **Create a Host Data Directory:**
   ```
   mkdir host-data
   ```
4. **Test Run a BioContainer (Get Help):**
   ```
   docker run biocontainers/blast:2.2.31 -help
   ```
5. In this example, we are using [BLAST](https://biocontainers.pro/tools/blast), which is an acronym for **Basic Local Alignment Search Tool**.
6. **List Downloaded Docker Images:**
   ```
   docker images
   ```
7. BioContainer images can be large. This is another benefit of using a Remote VM for these operations.
8. **Download and Unzip Data for BLAST (using Docker):**
   ```
   docker run --rm -v $(pwd)/host-data:/host-data biocontainers/wget:1.20.3 wget -P /host-data https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/blast-2.2.31-src.tar.gz
   ```
   **The video used `wget` to download a `.tar.gz` file. For a direct example of downloading a protein FASTA, replace the URL with a publicly available protein FASTA file.**
   - Unzip the downloaded protein file:
   ```
   docker run --rm -v $(pwd)/host-data:/host-data biocontainers/gzip:1.9 gzip -d /host-data/zebrafish.1.protein.faa.gz
   ```
9. **Verify Unzipped File:**
   ```
   ls host-data
   ```
   You should see `zebrafish.1.protein.faa`.
10. **Build a BLAST Protein Database:**
    ```
   docker run --rm -v $(pwd)/host-data:/host-data biocontainers/blast:2.2.31 makeblastdb -in /host-data/zebrafish.1.protein.faa -dbtype prot -out /host-data/zebrafish_db
   ```
11. **Download a Query Protein File:**
   ```
   docker run --rm -v $(pwd)/host-data:/host-data biocontainers/wget:1.20.3 wget -P /host-data https://www.uniprot.org/uniprot/P04156.fasta
   ```
12. **Verify Query File Download:**
   ```
   ls host-data
   ```
   You should now see `P04156.fasta` and your database files.
13. **Perform a BLAST Search:**
   ```
   docker run --rm -v $(pwd)/host-data:/host-data biocontainers/blast:2.2.31 blastp -query /host-data/P04156.fasta -db /host-data/zebrafish_db -out /host-data/results.txt
   ```

1. **View BLAST Results:**
   ```
   cat host-data/results.txt
   ```

The end user will now see the alignment details and scores for protein matches.

---

## Conclusion

In the [**previous blog**](https://docs.rafay.co/blog/2025/06/06/biocontainers-streamlining-bioinformatics-with-the-power-of-portability/), we reviewed how BioContainers represent a transformative leap forward for bioinformatics, offering unparalleled reproducibility, ease of use, and portability.

In this blog, we reviewed the steps data scientists can follow to successfully launch a remote VM, securely access it, and perform a basic bioinformatics task using BioContainers!