Please follow below instructions to submit a Dockerfile to biodockerfiles. The project biodockerfiles is maintained in GitHub so we are required to have a GitHub account to do a submission. Visit GitHub Signup page for creating a free account on GitHub.
Go to the directory in biodockerfiles GitHub repository that stores Dockerfiles. You may want to explore what Dockerfiles are available and how they are written.
Hit the Create new file button at the top to create a new Dockerfile under _dockerfiles/.
Type the name of the file as tool-version.md in the text field. Don’t forget to replace tool and version. Note that tool and version should have lowercase characters and separated by a hyphen (-) e.g. samtools-1.10.md.
Use the below template for our file.
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---
layout: default
title: tool-version
date: YYYY-MM-DD HH:MM +/-TTTT
excerpt: One sentence description of the tool
website: URL to the website of the tool
---
```dockerfile
# Here goes the Dockerfile
```
Add one sentence description to excerpt and type the tool’s website URL to website in the template. Then, add the Dockerfile within the triple backticks with dockerfile tag as shown in the place of # Here goes the Dockerfile in the template above.
Hit the Propose new file button at the end of the page to create the Dockerfile. This will fork the project and create the Dockerfile in a branch in the fork.
Then see the Comparing changes page and hit the Create pull request button (and then again in the following view) to actually submit the Dockerfile to biodockerfiles.
biodockerfiles is built with Jekyll so we need to setup Ruby and Bundler to use it. Go to Ruby installation page and bundler website for instructions to install them to our computer. We’ll also need git to be able to download the project and upload our submissions. Go to git installation page for instructions to install it. We also need GitHub’s command-line interface (CLI) for some of the operations such as forking a repository or creating a pull request. Go to GitHub CLI’s installation page to install it on our computer.
After everything is set up, open the Terminal and navigate to a directory that you want to keep biodockerfiles. Below commands are for *nix systems so please use Windows-counterparts when necessary.
Use below commands to fork the project biodockerfiles and clone the fork into our computer.
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cd ~/Desktop/
gh repo fork https://github.com/biodockerfiles/biodockerfiles.github.io.git --clone=true
cd biodockerfiles.github.io/
Now, we have the project and are inside it, we can install dependencies by running Bundler.
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bundle
After we installed the dependencies, we can create a new Dockerfile using Jekyll Compose.
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bundle exec jekyll compose "tool-version" --collection "dockerfiles"
Don’t forget to replace tool and version. Note that tool and version should have lowercase characters and separated by a hyphen (-) e.g. samtools-1.10.
This operation will create a file under _dockerfiles/ directory with the name tool-version.md. Open it with our favorite editor. Here we’ll be using Visual Studio Code.
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code _dockerfiles/tool-version.md
We will see a file as shown below.
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---
layout: default
title: tool-version
date: YYYY-MM-DD HH:MM +/-TTTT
excerpt:
website:
---
This information wrapped with --- is called front-matter and it contains metadata information about the Dockerfile. Most information will be added automatically. Add one sentence description to excerpt and type the tool’s website URL to website.
We then add the Dockerfile after the front-matter by wrapping it with triple backticks with dockerfile tag as shown below.
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```dockerfile
# Here goes the Dockerfile
```
So the entire content of _dockerfiles/tool-version.md will be as shown below.
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---
layout: default
title: tool-version
date: YYYY-MM-DD HH:MM +/-TTTT
excerpt: One sentence description of the tool
website: URL to the website of the tool
---
```dockerfile
# Here goes the Dockerfile
```
Alternatively, we can locally see how the Dockerfile look by running Jekyll as shown below.
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bundle exec jekyll serve
After running above command, go to http://localhost:4000/tool-version/ in our favorite browser to see how the Dockerfile looks.
Now, we created the file and can use git to push our Dockerfile to the forked repository.
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git add _dockerfiles/tool-version.md
git commit -m 'submitting tool-version'
git push origin master
Finally, we create a pull request to the original biodockerfiles repository to actually submit the Dockerfile.
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gh pr create -f -B https://github.com/biodockerfiles/biodockerfiles.github.io.git