diff --git a/.DS_Store b/.DS_Store deleted file mode 100644 index 99d58b3..0000000 Binary files a/.DS_Store and /dev/null differ diff --git a/docusaurus/blog/2019-05-28-first-blog-post.md b/docusaurus/blog/2019-05-28-first-blog-post.md deleted file mode 100644 index 02f3f81..0000000 --- a/docusaurus/blog/2019-05-28-first-blog-post.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -slug: first-blog-post -title: First Blog Post -authors: - name: Gao Wei - title: Docusaurus Core Team - url: https://github.com/wgao19 - image_url: https://github.com/wgao19.png -tags: [hola, docusaurus] ---- - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet diff --git a/docusaurus/blog/2019-05-29-long-blog-post.md b/docusaurus/blog/2019-05-29-long-blog-post.md deleted file mode 100644 index 26ffb1b..0000000 --- a/docusaurus/blog/2019-05-29-long-blog-post.md +++ /dev/null @@ -1,44 +0,0 @@ ---- -slug: long-blog-post -title: Long Blog Post -authors: endi -tags: [hello, docusaurus] ---- - -This is the summary of a very long blog post, - -Use a `` comment to limit blog post size in the list view. - - - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet diff --git a/docusaurus/blog/2020-12-01-welcome.md b/docusaurus/blog/2020-12-01-welcome.md deleted file mode 100644 index 50f9950..0000000 --- a/docusaurus/blog/2020-12-01-welcome.md +++ /dev/null @@ -1,14 +0,0 @@ ---- -slug: welcome -title: Welcome -author: Olivia Lang -author_title: Graduate Student @ CEGRcode -author_url: https://github.com/owlang -author_image_url: https://avatars.githubusercontent.com/u/15853523?s=60&v=4 -tags: [welcome, start] ---- - -Here's the first blog post for GenoPipe. We can post version updates or other news related to GenoPipe here. - -This blog is created with [**Docusaurus 2 alpha**](https://v2.docusaurus.io/). - diff --git a/docusaurus/blog/2021-08-01-mdx-blog-post.mdx b/docusaurus/blog/2021-08-01-mdx-blog-post.mdx deleted file mode 100644 index c04ebe3..0000000 --- a/docusaurus/blog/2021-08-01-mdx-blog-post.mdx +++ /dev/null @@ -1,20 +0,0 @@ ---- -slug: mdx-blog-post -title: MDX Blog Post -authors: [slorber] -tags: [docusaurus] ---- - -Blog posts support [Docusaurus Markdown features](https://docusaurus.io/docs/markdown-features), such as [MDX](https://mdxjs.com/). - -:::tip - -Use the power of React to create interactive blog posts. - -```js - -``` - - - -::: diff --git a/docusaurus/blog/2021-08-26-welcome/docusaurus-plushie-banner.jpeg b/docusaurus/blog/2021-08-26-welcome/docusaurus-plushie-banner.jpeg deleted file mode 100644 index 11bda09..0000000 Binary files a/docusaurus/blog/2021-08-26-welcome/docusaurus-plushie-banner.jpeg and /dev/null differ diff --git a/docusaurus/blog/2021-08-26-welcome/index.md b/docusaurus/blog/2021-08-26-welcome/index.md deleted file mode 100644 index 9455168..0000000 --- a/docusaurus/blog/2021-08-26-welcome/index.md +++ /dev/null @@ -1,25 +0,0 @@ ---- -slug: welcome -title: Welcome -authors: [slorber, yangshun] -tags: [facebook, hello, docusaurus] ---- - -[Docusaurus blogging features](https://docusaurus.io/docs/blog) are powered by the [blog plugin](https://docusaurus.io/docs/api/plugins/@docusaurus/plugin-content-blog). - -Simply add Markdown files (or folders) to the `blog` directory. - -Regular blog authors can be added to `authors.yml`. - -The blog post date can be extracted from filenames, such as: - -- `2019-05-30-welcome.md` -- `2019-05-30-welcome/index.md` - -A blog post folder can be convenient to co-locate blog post images: - -![Docusaurus Plushie](./docusaurus-plushie-banner.jpeg) - -The blog supports tags as well! - -**And if you don't want a blog**: just delete this directory, and use `blog: false` in your Docusaurus config. diff --git a/docusaurus/blog/authors.yml b/docusaurus/blog/authors.yml deleted file mode 100644 index bcb2991..0000000 --- a/docusaurus/blog/authors.yml +++ /dev/null @@ -1,17 +0,0 @@ -endi: - name: Endilie Yacop Sucipto - title: Maintainer of Docusaurus - url: https://github.com/endiliey - image_url: https://github.com/endiliey.png - -yangshun: - name: Yangshun Tay - title: Front End Engineer @ Facebook - url: https://github.com/yangshun - image_url: https://github.com/yangshun.png - -slorber: - name: Sébastien Lorber - title: Docusaurus maintainer - url: https://sebastienlorber.com - image_url: https://github.com/slorber.png diff --git a/docusaurus/docs/tutorial-basics/_category_.json b/docusaurus/docs/tutorial-basics/_category_.json deleted file mode 100644 index 2e6db55..0000000 --- a/docusaurus/docs/tutorial-basics/_category_.json +++ /dev/null @@ -1,8 +0,0 @@ -{ - "label": "Tutorial - Basics", - "position": 2, - "link": { - "type": "generated-index", - "description": "5 minutes to learn the most important Docusaurus concepts." - } -} diff --git a/docusaurus/docs/tutorial-basics/congratulations.md b/docusaurus/docs/tutorial-basics/congratulations.md deleted file mode 100644 index 9ef99bb..0000000 --- a/docusaurus/docs/tutorial-basics/congratulations.md +++ /dev/null @@ -1,21 +0,0 @@ ---- -sidebar_position: 6 ---- - -# Congratulations! - -You have just learned the **basics of Docusaurus** and made some changes to the **initial template**. - -Docusaurus has **much more to offer**! - -Have **5 more minutes**? Take a look at **[versioning](../tutorial-extras/manage-docs-versions.md)** and **[i18n](../tutorial-extras/translate-your-site.md)**. - -Anything **unclear** or **buggy** in this tutorial? [Please report it!](https://github.com/facebook/docusaurus/discussions/4610) - -## What's next? - -- Read the [official documentation](https://docusaurus.io/). -- Add a custom [Design and Layout](https://docusaurus.io/docs/styling-layout) -- Add a [search bar](https://docusaurus.io/docs/search) -- Find inspirations in the [Docusaurus showcase](https://docusaurus.io/showcase) -- Get involved in the [Docusaurus Community](https://docusaurus.io/community/support) diff --git a/docusaurus/docs/tutorial-basics/create-a-blog-post.md b/docusaurus/docs/tutorial-basics/create-a-blog-post.md deleted file mode 100644 index 0d50aaf..0000000 --- a/docusaurus/docs/tutorial-basics/create-a-blog-post.md +++ /dev/null @@ -1,34 +0,0 @@ ---- -sidebar_position: 3 ---- - -# Create a Blog Post - -Docusaurus creates a **page for each blog post**, but also a **blog index page**, a **tag system**, an **RSS** feed... - -## Create your first Post - -Create a file at `blog/2021-02-28-greetings.md`: - -```md title="blog/2021-02-28-greetings.md" ---- -slug: greetings -title: Greetings! -authors: - - name: Joel Marcey - title: Co-creator of Docusaurus 1 - url: https://github.com/JoelMarcey - image_url: https://github.com/JoelMarcey.png - - name: Sébastien Lorber - title: Docusaurus maintainer - url: https://sebastienlorber.com - image_url: https://github.com/slorber.png -tags: [greetings] ---- - -Congratulations, you have made your first post! - -Feel free to play around and edit this post as much you like. -``` - -A new blog post is now available at `http://localhost:3000/blog/greetings`. diff --git a/docusaurus/docs/tutorial-basics/create-a-document.md b/docusaurus/docs/tutorial-basics/create-a-document.md deleted file mode 100644 index a9bb9a4..0000000 --- a/docusaurus/docs/tutorial-basics/create-a-document.md +++ /dev/null @@ -1,55 +0,0 @@ ---- -sidebar_position: 2 ---- - -# Create a Document - -Documents are **groups of pages** connected through: - -- a **sidebar** -- **previous/next navigation** -- **versioning** - -## Create your first Doc - -Create a markdown file at `docs/hello.md`: - -```md title="docs/hello.md" -# Hello - -This is my **first Docusaurus document**! -``` - -A new document is now available at `http://localhost:3000/docs/hello`. - -## Configure the Sidebar - -Docusaurus automatically **creates a sidebar** from the `docs` folder. - -Add metadata to customize the sidebar label and position: - -```md title="docs/hello.md" {1-4} ---- -sidebar_label: 'Hi!' -sidebar_position: 3 ---- - -# Hello - -This is my **first Docusaurus document**! -``` - -It is also possible to create your sidebar explicitly in `sidebars.js`: - -```js title="sidebars.js" -module.exports = { - tutorialSidebar: [ - { - type: 'category', - label: 'Tutorial', - // highlight-next-line - items: ['hello'], - }, - ], -}; -``` diff --git a/docusaurus/docs/tutorial-basics/create-a-page.md b/docusaurus/docs/tutorial-basics/create-a-page.md deleted file mode 100644 index e112b00..0000000 --- a/docusaurus/docs/tutorial-basics/create-a-page.md +++ /dev/null @@ -1,43 +0,0 @@ ---- -sidebar_position: 1 ---- - -# Create a Page - -Add **Markdown or React** files to `src/pages` to create a **standalone page**: - -- `src/pages/index.js` -> `localhost:3000/` -- `src/pages/foo.md` -> `localhost:3000/foo` -- `src/pages/foo/bar.js` -> `localhost:3000/foo/bar` - -## Create your first React Page - -Create a file at `src/pages/my-react-page.js`: - -```jsx title="src/pages/my-react-page.js" -import React from 'react'; -import Layout from '@theme/Layout'; - -export default function MyReactPage() { - return ( - -

My React page

-

This is a React page

- - ); -} -``` - -A new page is now available at `http://localhost:3000/my-react-page`. - -## Create your first Markdown Page - -Create a file at `src/pages/my-markdown-page.md`: - -```mdx title="src/pages/my-markdown-page.md" -# My Markdown page - -This is a Markdown page -``` - -A new page is now available at `http://localhost:3000/my-markdown-page`. diff --git a/docusaurus/docs/tutorial-basics/deploy-your-site.md b/docusaurus/docs/tutorial-basics/deploy-your-site.md deleted file mode 100644 index 492eae0..0000000 --- a/docusaurus/docs/tutorial-basics/deploy-your-site.md +++ /dev/null @@ -1,31 +0,0 @@ ---- -sidebar_position: 5 ---- - -# Deploy your site - -Docusaurus is a **static-site-generator** (also called **[Jamstack](https://jamstack.org/)**). - -It builds your site as simple **static HTML, JavaScript and CSS files**. - -## Build your site - -Build your site **for production**: - -```bash -npm run build -``` - -The static files are generated in the `build` folder. - -## Deploy your site - -Test your production build locally: - -```bash -npm run serve -``` - -The `build` folder is now served at `http://localhost:3000/`. - -You can now deploy the `build` folder **almost anywhere** easily, **for free** or very small cost (read the **[Deployment Guide](https://docusaurus.io/docs/deployment)**). diff --git a/docusaurus/docs/tutorial-basics/markdown-features.mdx b/docusaurus/docs/tutorial-basics/markdown-features.mdx deleted file mode 100644 index 6b3aaaa..0000000 --- a/docusaurus/docs/tutorial-basics/markdown-features.mdx +++ /dev/null @@ -1,146 +0,0 @@ ---- -sidebar_position: 4 ---- - -# Markdown Features - -Docusaurus supports **[Markdown](https://daringfireball.net/projects/markdown/syntax)** and a few **additional features**. - -## Front Matter - -Markdown documents have metadata at the top called [Front Matter](https://jekyllrb.com/docs/front-matter/): - -```text title="my-doc.md" -// highlight-start ---- -id: my-doc-id -title: My document title -description: My document description -slug: /my-custom-url ---- -// highlight-end - -## Markdown heading - -Markdown text with [links](./hello.md) -``` - -## Links - -Regular Markdown links are supported, using url paths or relative file paths. - -```md -Let's see how to [Create a page](/create-a-page). -``` - -```md -Let's see how to [Create a page](./create-a-page.md). -``` - -**Result:** Let's see how to [Create a page](./create-a-page.md). - -## Images - -Regular Markdown images are supported. - -You can use absolute paths to reference images in the static directory (`static/img/docusaurus.png`): - -```md -![Docusaurus logo](/img/docusaurus.png) -``` - -![Docusaurus logo](/img/docusaurus.png) - -You can reference images relative to the current file as well, as shown in [the extra guides](../tutorial-extras/manage-docs-versions.md). - -## Code Blocks - -Markdown code blocks are supported with Syntax highlighting. - - ```jsx title="src/components/HelloDocusaurus.js" - function HelloDocusaurus() { - return ( -

Hello, Docusaurus!

- ) - } - ``` - -```jsx title="src/components/HelloDocusaurus.js" -function HelloDocusaurus() { - return

Hello, Docusaurus!

; -} -``` - -## Admonitions - -Docusaurus has a special syntax to create admonitions and callouts: - - :::tip My tip - - Use this awesome feature option - - ::: - - :::danger Take care - - This action is dangerous - - ::: - -:::tip My tip - -Use this awesome feature option - -::: - -:::danger Take care - -This action is dangerous - -::: - -## MDX and React Components - -[MDX](https://mdxjs.com/) can make your documentation more **interactive** and allows using any **React components inside Markdown**: - -```jsx -export const Highlight = ({children, color}) => ( - { - alert(`You clicked the color ${color} with label ${children}`) - }}> - {children} - -); - -This is Docusaurus green ! - -This is Facebook blue ! -``` - -export const Highlight = ({children, color}) => ( - { - alert(`You clicked the color ${color} with label ${children}`); - }}> - {children} - -); - -This is Docusaurus green ! - -This is Facebook blue ! diff --git a/docusaurus/docs/tutorial-extras/_category_.json b/docusaurus/docs/tutorial-extras/_category_.json deleted file mode 100644 index a8ffcc1..0000000 --- a/docusaurus/docs/tutorial-extras/_category_.json +++ /dev/null @@ -1,7 +0,0 @@ -{ - "label": "Tutorial - Extras", - "position": 3, - "link": { - "type": "generated-index" - } -} diff --git a/docusaurus/docs/tutorial-extras/img/docsVersionDropdown.png b/docusaurus/docs/tutorial-extras/img/docsVersionDropdown.png deleted file mode 100644 index 97e4164..0000000 Binary files a/docusaurus/docs/tutorial-extras/img/docsVersionDropdown.png and /dev/null differ diff --git a/docusaurus/docs/tutorial-extras/img/localeDropdown.png b/docusaurus/docs/tutorial-extras/img/localeDropdown.png deleted file mode 100644 index e257edc..0000000 Binary files a/docusaurus/docs/tutorial-extras/img/localeDropdown.png and /dev/null differ diff --git a/docusaurus/docs/tutorial-extras/manage-docs-versions.md b/docusaurus/docs/tutorial-extras/manage-docs-versions.md deleted file mode 100644 index e12c3f3..0000000 --- a/docusaurus/docs/tutorial-extras/manage-docs-versions.md +++ /dev/null @@ -1,55 +0,0 @@ ---- -sidebar_position: 1 ---- - -# Manage Docs Versions - -Docusaurus can manage multiple versions of your docs. - -## Create a docs version - -Release a version 1.0 of your project: - -```bash -npm run docusaurus docs:version 1.0 -``` - -The `docs` folder is copied into `versioned_docs/version-1.0` and `versions.json` is created. - -Your docs now have 2 versions: - -- `1.0` at `http://localhost:3000/docs/` for the version 1.0 docs -- `current` at `http://localhost:3000/docs/next/` for the **upcoming, unreleased docs** - -## Add a Version Dropdown - -To navigate seamlessly across versions, add a version dropdown. - -Modify the `docusaurus.config.js` file: - -```js title="docusaurus.config.js" -module.exports = { - themeConfig: { - navbar: { - items: [ - // highlight-start - { - type: 'docsVersionDropdown', - }, - // highlight-end - ], - }, - }, -}; -``` - -The docs version dropdown appears in your navbar: - -![Docs Version Dropdown](./img/docsVersionDropdown.png) - -## Update an existing version - -It is possible to edit versioned docs in their respective folder: - -- `versioned_docs/version-1.0/hello.md` updates `http://localhost:3000/docs/hello` -- `docs/hello.md` updates `http://localhost:3000/docs/next/hello` diff --git a/docusaurus/docs/tutorial-extras/translate-your-site.md b/docusaurus/docs/tutorial-extras/translate-your-site.md deleted file mode 100644 index da2b8a3..0000000 --- a/docusaurus/docs/tutorial-extras/translate-your-site.md +++ /dev/null @@ -1,88 +0,0 @@ ---- -sidebar_position: 2 ---- - -# Translate your site - -Let's translate `docs/intro.md` to French. - -## Configure i18n - -Modify `docusaurus.config.js` to add support for the `fr` locale: - -```js title="docusaurus.config.js" -module.exports = { - i18n: { - defaultLocale: 'en', - locales: ['en', 'fr'], - }, -}; -``` - -## Translate a doc - -Copy the `docs/intro.md` file to the `i18n/fr` folder: - -```bash -mkdir -p i18n/fr/docusaurus-plugin-content-docs/current/ - -cp docs/intro.md i18n/fr/docusaurus-plugin-content-docs/current/intro.md -``` - -Translate `i18n/fr/docusaurus-plugin-content-docs/current/intro.md` in French. - -## Start your localized site - -Start your site on the French locale: - -```bash -npm run start -- --locale fr -``` - -Your localized site is accessible at `http://localhost:3000/fr/` and the `Getting Started` page is translated. - -:::caution - -In development, you can only use one locale at a same time. - -::: - -## Add a Locale Dropdown - -To navigate seamlessly across languages, add a locale dropdown. - -Modify the `docusaurus.config.js` file: - -```js title="docusaurus.config.js" -module.exports = { - themeConfig: { - navbar: { - items: [ - // highlight-start - { - type: 'localeDropdown', - }, - // highlight-end - ], - }, - }, -}; -``` - -The locale dropdown now appears in your navbar: - -![Locale Dropdown](./img/localeDropdown.png) - -## Build your localized site - -Build your site for a specific locale: - -```bash -npm run build -- --locale fr -``` - -Or build your site to include all the locales at once: - -```bash -npm run build -``` diff --git a/docusaurus/docusaurus.config.js b/docusaurus/docusaurus.config.js index 6870f7f..f746b07 100644 --- a/docusaurus/docusaurus.config.js +++ b/docusaurus/docusaurus.config.js @@ -1,53 +1,51 @@ // @ts-check // Note: type annotations allow type checking and IDEs autocompletion -const lightCodeTheme = require('prism-react-renderer/themes/github'); -const darkCodeTheme = require('prism-react-renderer/themes/dracula'); +const lightCodeTheme = require("prism-react-renderer/themes/github"); +const darkCodeTheme = require("prism-react-renderer/themes/dracula"); /** @type {import('@docusaurus/types').Config} */ const config = { - title: 'GenoPipe', - tagline: 'Run a background check on your NGS data', - url: 'https://github.com/CEGRcode', - baseUrl: '/GenoPipe/', - onBrokenLinks: 'throw', - onBrokenMarkdownLinks: 'warn', - favicon: 'genopipe-img/logo.png', + title: "GenoPipe", + tagline: "Run a background check on your NGS data", + url: "https://github.com/CEGRcode", + baseUrl: "/GenoPipe/", + onBrokenLinks: "throw", + onBrokenMarkdownLinks: "warn", + favicon: "img/genopipe.ico", // GitHub pages deployment config. // If you aren't using GitHub pages, you don't need these. - organizationName: 'CEGRcode', // Usually your GitHub org/user name. - projectName: 'GenoPipe', // Usually your repo name. + organizationName: "CEGRcode", // Usually your GitHub org/user name. + projectName: "GenoPipe", // Usually your repo name. // Even if you don't use internalization, you can use this field to set useful // metadata like html lang. For example, if your site is Chinese, you may want // to replace "en" with "zh-Hans". i18n: { - defaultLocale: 'en', - locales: ['en'], + defaultLocale: "en", + locales: ["en"], }, presets: [ [ - 'classic', + "classic", /** @type {import('@docusaurus/preset-classic').Options} */ ({ docs: { - sidebarPath: require.resolve('./sidebars.js'), + sidebarPath: require.resolve("./sidebars.js"), // Please change this to your repo. // Remove this to remove the "edit this page" links. - editUrl: - 'https://github.com/CEGRcode/GenoPipe', + editUrl: "https://github.com/CEGRcode/GenoPipe", }, blog: { showReadingTime: true, // Please change this to your repo. // Remove this to remove the "edit this page" links. - editUrl: - 'https://github.com/CEGRcode/GenoPipe', + editUrl: "https://github.com/CEGRcode/GenoPipe", }, theme: { - customCss: require.resolve('./src/css/custom.css'), + customCss: require.resolve("./src/css/custom.css"), }, }), ], @@ -57,94 +55,95 @@ const config = { /** @type {import('@docusaurus/preset-classic').ThemeConfig} */ ({ navbar: { - title: 'GenoPipe', + title: "GenoPipe", logo: { - alt: 'GenoPipe Logo', - src: 'genopipe-img/logo.png', + alt: "GenoPipe Logo", + src: "img/genopipe.png", }, items: [ { - type: 'doc', - docId: 'welcome', - position: 'left', - label: 'General', + type: "doc", + docId: "welcome", + position: "left", + label: "General", }, - { - type: 'doc', - docId: 'epitopeid', - position: 'left', - label: 'EpitopeID', - }, - { - type: 'doc', - docId: 'deletionid', - position: 'left', - label: 'DeletionID', - }, - { - type: 'doc', - docId: 'strainid', - position: 'left', - label: 'StrainID', - }, { - href: 'https://github.com/CEGRcode/GenoPipe', - label: 'GitHub', - position: 'right', + type: "doc", + docId: "epitopeid", + position: "left", + label: "EpitopeID", + }, + { + type: "doc", + docId: "deletionid", + position: "left", + label: "DeletionID", + }, + { + type: "doc", + docId: "strainid", + position: "left", + label: "StrainID", + }, + { + href: "https://github.com/CEGRcode/GenoPipe", + /*label: "GitHub",*/ + position: "right", + className: "header-github-link", }, ], }, footer: { - style: 'dark', + style: "dark", links: [ { - title: 'Module Docs', + title: "Module Docs", items: [ { - label: 'EpitopeID', - to: '/docs/epitopeid', + label: "EpitopeID", + to: "/docs/epitopeid", }, { - label: 'DeletionID', - to: '/docs/deletionid', + label: "DeletionID", + to: "/docs/deletionid", }, { - label: 'StrainID', - to: '/docs/strainid', + label: "StrainID", + to: "/docs/strainid", }, ], }, { - title: 'Community', + title: "Community", items: [ { - label: 'Pugh Lab Website', - href: 'https://pughlab.mbg.cornell.edu/', + label: "Pugh Lab Website", + href: "https://pughlab.mbg.cornell.edu/", }, { - label: 'Lai Lab', - href: 'https://williamkmlai.github.io', + label: "Lai Lab", + href: "https://williamkmlai.github.io", }, ], }, { - title: 'Other Tools We Develop', + title: "Other Tools We Develop", items: [ { - label: 'ScriptManager', - href: 'https://github.com/CEGRcode/scriptmanager', + label: "ScriptManager", + href: "https://github.com/CEGRcode/scriptmanager", }, { - label: 'PEGR', - href: 'https://github.com/seqcode/pegr', + label: "PEGR", + href: "https://github.com/seqcode/pegr", }, { - label: 'STENCIL', - href: 'https://github.com/CEGRcode/stencil', + label: "STENCIL", + href: "https://github.com/CEGRcode/stencil", }, { - label: 'GenoPipe', - href: 'https://github.com/CEGRcode/GenoPipe', + label: "GenoPipe", + href: "https://github.com/CEGRcode/GenoPipe", }, ], }, diff --git a/docusaurus/src/components/HomepageFeatures/index.js b/docusaurus/src/components/HomepageFeatures/index.js index 76c3af1..ad8d74f 100644 --- a/docusaurus/src/components/HomepageFeatures/index.js +++ b/docusaurus/src/components/HomepageFeatures/index.js @@ -1,38 +1,40 @@ -import React from 'react'; -import clsx from 'clsx'; -import styles from './styles.module.css'; -import { translate } from '@docusaurus/Translate'; +import React from "react"; +import clsx from "clsx"; +import styles from "./styles.module.css"; +import { translate } from "@docusaurus/Translate"; const FeatureList = [ { - title: 'EpitopeID', - Svg: require('@site/static/genopipe-img/EpitopeID_icon2.svg').default, + title: "EpitopeID", + Svg: require("@site/static/genopipe-img/EpitopeID_icon.svg").default, description: ( <> - Check your FASTQ files to confirm epitope sequence insertions in genomic DNA. + Check your FASTQ files to confirm epitope sequence insertions in genomic + DNA. ), - link:"docs/epitopeid" + link: "docs/epitopeid", }, { - title: 'DeletionID', - Svg: require('@site/static/genopipe-img/DeletionID_icon2.svg').default, + title: "DeletionID", + Svg: require("@site/static/genopipe-img/DeletionID_icon.svg").default, description: ( <> Check your BAM files for regions with significant depletions of reads. ), - link:"docs/deletionid" + link: "docs/deletionid", }, { - title: 'StrainID', - Svg: require('@site/static/genopipe-img/StrainID_icon2.svg').default, + title: "StrainID", + Svg: require("@site/static/genopipe-img/StrainID_icon.svg").default, description: ( <> - Check your BAM files for variants and see which strain your sample most closely resembles. + Check your BAM files for variants and see which strain your sample most + closely resembles. ), - link:"docs/strainid" + link: "docs/strainid", }, ]; @@ -50,20 +52,43 @@ const FeatureList = [ ); }*/ - -function Feature({Svg, title, description,link}) { +function Feature({ Svg, title, description, link }) { return ( -
-
+
+
- +
-

{title}

-

{description}

+

{title}

+

{description}

- Read More + + Read More + +
diff --git a/docusaurus/src/css/custom.css b/docusaurus/src/css/custom.css index 372ffbf..f7bc983 100644 --- a/docusaurus/src/css/custom.css +++ b/docusaurus/src/css/custom.css @@ -28,3 +28,16 @@ --ifm-color-primary-lightest: #0ca6e3; --docusaurus-highlighted-code-line-bg: rgba(0, 0, 0, 0.3); } + +.header-github-link:hover { + opacity: 0.6; +} + +.header-github-link:before { + background: url("data:image/svg+xml;charset=utf-8,%3Csvg viewBox='0 0 24 24' xmlns='http://www.w3.org/2000/svg'%3E%3Cpath d='M12 .297c-6.63 0-12 5.373-12 12 0 5.303 3.438 9.8 8.205 11.385.6.113.82-.258.82-.577 0-.285-.01-1.04-.015-2.04-3.338.724-4.042-1.61-4.042-1.61C4.422 18.07 3.633 17.7 3.633 17.7c-1.087-.744.084-.729.084-.729 1.205.084 1.838 1.236 1.838 1.236 1.07 1.835 2.809 1.305 3.495.998.108-.776.417-1.305.76-1.605-2.665-.3-5.466-1.332-5.466-5.93 0-1.31.465-2.38 1.235-3.22-.135-.303-.54-1.523.105-3.176 0 0 1.005-.322 3.3 1.23.96-.267 1.98-.399 3-.405 1.02.006 2.04.138 3 .405 2.28-1.552 3.285-1.23 3.285-1.23.645 1.653.24 2.873.12 3.176.765.84 1.23 1.91 1.23 3.22 0 4.61-2.805 5.625-5.475 5.92.42.36.81 1.096.81 2.22 0 1.606-.015 2.896-.015 3.286 0 .315.21.69.825.57C20.565 22.092 24 17.592 24 12.297c0-6.627-5.373-12-12-12'/%3E%3C/svg%3E") + no-repeat; + content: ""; + display: flex; + height: 24px; + width: 24px; +} diff --git a/docusaurus/src/pages/index.js b/docusaurus/src/pages/index.js index a9845e8..a57fd48 100644 --- a/docusaurus/src/pages/index.js +++ b/docusaurus/src/pages/index.js @@ -1,18 +1,17 @@ -import React from 'react'; -import clsx from 'clsx'; -import Layout from '@theme/Layout'; -import Link from '@docusaurus/Link'; -import useDocusaurusContext from '@docusaurus/useDocusaurusContext'; -import styles from './index.module.css'; -import HomepageFeatures from '@site/src/components/HomepageFeatures'; +import React from "react"; +import clsx from "clsx"; +import Layout from "@theme/Layout"; +import Link from "@docusaurus/Link"; +import useDocusaurusContext from "@docusaurus/useDocusaurusContext"; +import styles from "./index.module.css"; +import HomepageFeatures from "@site/src/components/HomepageFeatures"; function HomepageHeader() { - const {siteConfig} = useDocusaurusContext(); + const { siteConfig } = useDocusaurusContext(); return ( - -
+
- +

{siteConfig.title}

@@ -20,22 +19,23 @@ function HomepageHeader() {
+ to="/docs/welcome" + > Get Started
-
); } export default function Home() { - const {siteConfig} = useDocusaurusContext(); + const { siteConfig } = useDocusaurusContext(); return ( + description="Description will go into a meta tag in " + >
diff --git a/docusaurus/src/pages/index.module.css b/docusaurus/src/pages/index.module.css index 8cd2642..ac075a9 100644 --- a/docusaurus/src/pages/index.module.css +++ b/docusaurus/src/pages/index.module.css @@ -16,9 +16,14 @@ z-index: 1; left: 5px; margin: auto; /*max-width: 1400px;*/ - width: 200%; - opacity: .4; + width: 100%; + background: no-repeat center center fixed; + opacity: .35; position: absolute; + -webkit-background-size: cover; + -moz-background-size: cover; + -o-background-size: cover; + background-size: cover; right: 0; top: -10px; z-index:-10; @@ -43,3 +48,4 @@ z-index: 1; align-items: center; justify-content: center; } + diff --git a/docusaurus/static/genopipe-img/DeletionID_icon2.svg b/docusaurus/static/genopipe-img/DeletionID_icon.svg similarity index 100% rename from docusaurus/static/genopipe-img/DeletionID_icon2.svg rename to docusaurus/static/genopipe-img/DeletionID_icon.svg diff --git a/docusaurus/static/genopipe-img/EpitopeID_icon2.svg b/docusaurus/static/genopipe-img/EpitopeID_icon.svg similarity index 100% rename from docusaurus/static/genopipe-img/EpitopeID_icon2.svg rename to docusaurus/static/genopipe-img/EpitopeID_icon.svg diff --git a/docusaurus/static/genopipe-img/StrainID_icon2.svg b/docusaurus/static/genopipe-img/StrainID_icon.svg similarity index 100% rename from docusaurus/static/genopipe-img/StrainID_icon2.svg rename to docusaurus/static/genopipe-img/StrainID_icon.svg diff --git a/docusaurus/static/genopipe-img/deletionid-icon.png b/docusaurus/static/genopipe-img/deletionid-icon.png deleted file mode 100644 index 88afc96..0000000 Binary files a/docusaurus/static/genopipe-img/deletionid-icon.png and /dev/null differ diff --git a/docusaurus/static/genopipe-img/epitopeid-icon.png b/docusaurus/static/genopipe-img/epitopeid-icon.png deleted file mode 100644 index 4ed087f..0000000 Binary files a/docusaurus/static/genopipe-img/epitopeid-icon.png and /dev/null differ diff --git a/docusaurus/static/genopipe-img/strainid-icon.png b/docusaurus/static/genopipe-img/strainid-icon.png deleted file mode 100644 index 2db0591..0000000 Binary files a/docusaurus/static/genopipe-img/strainid-icon.png and /dev/null differ diff --git a/docusaurus/static/img/background.png b/docusaurus/static/img/background.png new file mode 100644 index 0000000..13e3ff8 Binary files /dev/null and b/docusaurus/static/img/background.png differ diff --git a/docusaurus/static/img/background_png_1@4x.png b/docusaurus/static/img/background_png_1@4x.png deleted file mode 100644 index eabf231..0000000 Binary files a/docusaurus/static/img/background_png_1@4x.png and /dev/null differ diff --git a/docusaurus/static/img/docusaurus.png b/docusaurus/static/img/docusaurus.png deleted file mode 100644 index f458149..0000000 Binary files a/docusaurus/static/img/docusaurus.png and /dev/null differ diff --git a/docusaurus/static/img/favicon.ico b/docusaurus/static/img/favicon.ico deleted file mode 100644 index c01d54b..0000000 Binary files a/docusaurus/static/img/favicon.ico and /dev/null differ diff --git a/docusaurus/static/img/genopipe.ico b/docusaurus/static/img/genopipe.ico new file mode 100644 index 0000000..045efd9 Binary files /dev/null and b/docusaurus/static/img/genopipe.ico differ diff --git a/docusaurus/static/genopipe-img/logo.png b/docusaurus/static/img/genopipe.png similarity index 100% rename from docusaurus/static/genopipe-img/logo.png rename to docusaurus/static/img/genopipe.png diff --git a/docusaurus/static/img/logo.svg b/docusaurus/static/img/logo.svg deleted file mode 100644 index 9db6d0d..0000000 --- a/docusaurus/static/img/logo.svg +++ /dev/null @@ -1 +0,0 @@ - \ No newline at end of file diff --git a/docusaurus/static/img/undraw_docusaurus_mountain.svg b/docusaurus/static/img/undraw_docusaurus_mountain.svg deleted file mode 100644 index af961c4..0000000 --- a/docusaurus/static/img/undraw_docusaurus_mountain.svg +++ /dev/null @@ -1,171 +0,0 @@ - - Easy to Use - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/docusaurus/static/img/undraw_docusaurus_react.svg b/docusaurus/static/img/undraw_docusaurus_react.svg deleted file mode 100644 index 94b5cf0..0000000 --- a/docusaurus/static/img/undraw_docusaurus_react.svg +++ /dev/null @@ -1,170 +0,0 @@ - - Powered by React - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/docusaurus/static/img/undraw_docusaurus_tree.svg b/docusaurus/static/img/undraw_docusaurus_tree.svg deleted file mode 100644 index d9161d3..0000000 --- a/docusaurus/static/img/undraw_docusaurus_tree.svg +++ /dev/null @@ -1,40 +0,0 @@ - - Focus on What Matters - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -