Merge pull request #156 from JotaKas/main

Update 03-software-containers.md

docs/_Reproducible-Data-Analysis/03-software-containers.md

@@ -5,3 +5,86 @@ layout: default
 docs_css: markdown
 empty: true
 ---
+
+# Software Containers
+
+## Introduction to Software Containers
+Software containers, such as [Apptainer](https://apptainer.org/) (formerly known as Singularity) and [Docker](https://www.docker.com/) provide a way to encapsulate an application and its environment for consistent, portable, and reproducible execution across various computing environments.
+This is crucial for scientific research, ensuring that analyses remain consistent regardless of the underlying infrastructure.
+
+## Why Use Software Containers?
+- **Consistency and Reproducibility**: Containers ensure your analysis runs the same way, everywhere.
+- **Isolation**: Package your application with its dependencies to avoid conflicts.
+- **Portability**: Easily share your computational environment with others.
+
+## Getting Started with Containers
+Apptainer is a popular choice in scientific and high-performance computing (HPC) environments due to its ability to handle container privileges.
+It offers secure, user-friendly containerization, making it ideal for computational biology and bioinformatics.
+Based on the same technology, Docker images are compatible with Apptainer and most commands function similarly.
+
+NFDI4Microbiota recommends that researchers start out with Apptainer if you are not bound to a docker environment, because it is usually much easier and nudges you to follow the [best practices] by default.
+
+For installation and quick start, always refer to the main documenation page from the containirazation software of choice.
+
+[Apptainer Quick Start](https://apptainer.org/docs/user/latest/quick_start.html)
+[Docker Quick Start](https://docs.docker.com/guides/get-started/)
+
+
+## Example of Working with Containers
+
+### Apptainer
+To start getting an idea what a container actually is, it is relevant to get some examples.
+A good example of a software available as a apptainer container is [Virsorter2](https://github.com/jiarong/VirSorter2), a multi-classifier with an expert-guided approach to detect diverse DNA and RNA virus genomes.
+
+Running VirSorter2 using Apptainer looks like:
+```sh
+$ apptainer build virsorter2.sif docker://jiarong/virsorter:latest
+```
+You will get a file `virsorter2.sif`, which is a apptainer image that can be run like a binary executable file.
+You can use the absolute path of this file to replace Virsorter2 in commands.
+Also this image has the database and dependencies included, so you can skip the download of databases and dependencies.
+
+### Docker
+Similarly with Docker, the user can find an example of running BLAST [here](https://biocontainers-edu.readthedocs.io/en/latest/running_example.html)
+
+
+## Best Practices for Container Creation {best-practices}
+When creating containers, incorporating best practices ensures efficiency, security, and reproducibility. Here's a concise guide, drawing from broader container best practices, including insights from [Google Cloud's recommendations](https://cloud.google.com/architecture/best-practices-for-building-containers):
+
+- **Use Specific Versions**: Specify exact versions of base images, software, and libraries, in order to avoid breaking changes occuring when updating with the `latest` tag and ensures consistency across environments.
+
+- **Minimize Layer Size**: Structure your definition file to combine related commands into single layers to reduce the container size which speeds up download and deployment.
+
+- **Clean Up**: Remove unnecessary packages and clear cache in the same layer where installations occur to minimize the container's footprint.
+
+- **Non-root User**: Run the container as a non-root user whenever possible, which enhances the security of the container, reducing the risk of privilege escalation attacks.
+
+- **Base Image Selection**: Choose a minimal base image that includes only the necessary packages and libraries for your application, to minimizes the attack surface and the container size.
+
+- **Immutable Containers**: Treat containers as immutable.
+For updates or changes, build a new container image.
+This facilitates modularity and version control while ensuring reproducibility.
+
+- **Security Scanning**: Regularly scan your containers for vulnerabilities and apply patches as needed.
+Keeping your containers updated is crucial for security.
+
+- **Efficient Data Management**: Store data and logs outside of containers to ensure persistence and scalability.
+Use volumes or bind mounts for data that needs to persist beyond the life of the container.
+
+- **Documentation**: Include a `%help` section in your definition file, providing users with information on how to use the container, including running the software and accessing data.
+
+
+## Advanced Usage
+#### [Integration with Nextflow](https://www.nextflow.io/docs/latest/container.html)
+- **Nextflow and Containers**: Simplifies complex workflows by executing each step in a container for consistency across environments.
+- **Configurations**: Supports managing containers through `nextflow.config`, streamlining execution.
+
+#### [Kubernetes and Containers](https://kubernetes.io/docs/home/)
+- **Container Orchestration**: Automates deployment, scaling, and management of containerized applications, essential for microservices architecture.
+- **Scalability and Management**: Provides tools for load balancing, auto-scaling, and efficient resource allocation across diverse infrastructures.
+
+## Resources and Further Reading
+- [Apptainer User Guide](https://apptainer.org/docs/user/latest/introduction.html): Comprehensive documentation for getting started with Apptainer.
+- [BioContainers Community](https://biocontainers.pro/): A resource for finding and sharing containerized bioinformatics tools.
+- [Docker Introduction Lesson (Beta version)](https://carpentries-incubator.github.io/docker-introduction/)
+- [Singularity Introduction (Alpha version)](https://carpentries-incubator.github.io/singularity-introduction/)