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# apptainerce_build
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为了创建一个模块化、易于维护的 Shell 脚本来自动安装 Apptainer (SingularityCE 的社区版本)，我们可以将脚本分为几个部分：安装依赖、安装 Go、下载和编译 Apptainer，以及卸载功能。同时，我们将使用变量来控制版本号和下载链接，使得维护和更新更加方便。
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## apptainer
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## Getting started
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Singularity和Apptainer 区别
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To make it easy for you to get started with GitLab, here's a list of recommended next steps.
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Singularity和Apptainer是同一款软件的不同版本。Singularity是一款流行的容器技术，专为高性能计算（HPC）和数据密集型应用设计。它允许用户在单个文件中打包软件应用程序和所有相关的依赖项，以便在其他系统上无缝运行。
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Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
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然而，Singularity的开发和维护是由Sylabs进行的，这是一家商业公司。在2021年，Sylabs决定将Singularity的开发转向更商业化的方向，这引发了社区的一些争议。
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## Add your files
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为了保持Singularity的开源和社区驱动的本质，Singularity的原始开发者和社区成员决定创建一个新的项目，名为Apptainer。Apptainer是Singularity的一个分支，其目标是继续开发和维护一个完全开源和社区驱动的容器技术。
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- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
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- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
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总的来说，Singularity和Apptainer都是相同的容器技术，只是由于开发和维护的策略差异，导致了两个不同的项目。
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```
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cd existing_repo
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git remote add origin http://gitlab.dockless.eu.org/lingyuzeng/apptainerce_build.git
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git branch -M main
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git push -uf origin main
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### Apptainer封装原则
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- 数据库，容器分离原则，降低耦合度，复用数据库。
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- 编译和封装分离原则，软件编译可以在容器内也可以在容器外，编译完再安装到全新的基础镜像。
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- 尽量使用编译型语言写脚本，可以减小容器体积，**Python，Perl** 等解释器也会占不少体积。
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- 保持版本记录，每个镜像文件都匹配一个**Definition**文件，里面能标注准确标注版本号就尽量标注。
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- 如果需要使用 **conda**，选择 **micromamba。**
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首先，生物信息数据分析属于 **HPC** 计算范畴，很适合集群环境，容器可以隔离每个软件的运行环境，让不同软件拥有独立的依赖关系，其实 Conda 也可以做到环境的隔离，但是 **conda** 有其自身的问题，这里不讨论。可以选择 **Docker**（https://www.docker.com/） 或者 **Apptainer**（https://apptainer.org/，先前叫 Singularity ）, 根据文章标题可以看出，最后推荐 **Apptainer**，几点好处：
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- 可以生成单一的 **sif** 文件，方便直接以文件的形式部署和分享，在服务集群上各个节点可以直接调用容器。
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- 可以直接使用 **DockerHub** 的 镜像生成 **sif** 文件
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- 使用 **alpine** 直接使用编译后的文件，可以将镜像文件做的很小，接近 **2M** 左右。
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- 创建和使用容器不再需要管理员权限。
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几点心得：
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- 尽量使用国内镜像。
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- 构建本地的 **HTTP** 服务器，保证构建镜像构建过程稳定。
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- 非通用的数据库，数据库可以考虑和容器打包放在一起，版本也好控制。
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- 一些软件可能不无法在 **alpine** 基础进行安装成功，比如 **BLAST**
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- 推荐 **Rocky Linux 9.2** 基础镜像，体积大约 **60M**
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- 如果封装 **R** 程序, 可以使用 **r-base** 基础镜像库，体积比较小。
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- 能用编译型编程语言写程序尽量不用解释型语言写，安装额外的语言执行环境会让容器体积变大。
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- 学会自己构建镜像，**Github** 上提供的 **Dockerfile** 不一定会真的工作。
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# 使用Apptainer本地镜像文件构建容器
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使用本地镜像文件会出现：
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1. 网络稳定性问题
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2. 镜像文件太大，导致传输失败
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### 基础镜像
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```text
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alpine https://hub.docker.com/_/alpine，体积只有 **3M**
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RockyLinux https://hub.docker.com/_/rockyinux
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Ubuntu https://hub.docker.com/_/ubuntu
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CentOS https://hub.docker.com/_/centos
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R-base https://hub.docker.com/_/r-base
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```
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## Integrate with your tools
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- [ ] [Set up project integrations](http://gitlab.dockless.eu.org/lingyuzeng/apptainerce_build/-/settings/integrations)
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## Collaborate with your team
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- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
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- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
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- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
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- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
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- [ ] [Set auto-merge](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
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## Test and Deploy
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Use the built-in continuous integration in GitLab.
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- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
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- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing (SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
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- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
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- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
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- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
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***
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# Editing this README
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When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thanks to [makeareadme.com](https://www.makeareadme.com/) for this template.
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## Suggestions for a good README
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Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
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## Name
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Choose a self-explaining name for your project.
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## Description
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Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
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## Badges
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On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
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## Visuals
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Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
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## Installation
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Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
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## Usage
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Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
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## Support
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Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
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## Roadmap
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If you have ideas for releases in the future, it is a good idea to list them in the README.
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## Contributing
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State if you are open to contributions and what your requirements are for accepting them.
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For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
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You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
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## Authors and acknowledgment
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Show your appreciation to those who have contributed to the project.
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## License
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For open source projects, say how it is licensed.
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## Project status
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If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
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使用 **Docker Hub** 的基础镜像无法正常构建容器，应该是 **DNS** 问题导致，这类网络导致的问题其实挺麻烦，解决的问题的最佳方案就是本地化基础镜像库。
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