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initial commit - templated book
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‎.copier-answers.yml‎

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# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
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_commit: 87f724d
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_src_path: https://github.com/gregcaporaso/q2docs-template
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author_website: https://cap-lab.bio
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book_author: Greg Caporaso
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book_id: news.rachis.org
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book_title: rachis project news
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book_type: Plugin documentation
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plugin_name: news.rachis.org

‎.gitignore‎

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book/references/plugin-reference
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book/references/q2doc.bib
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book/_build/
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book/data/
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.locks/
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.DS_Store

‎.readthedocs.yml‎

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# Read the Docs configuration file
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# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
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# Required
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version: 2
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# Set the OS, Python version, and other tools you might need
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build:
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os: ubuntu-24.04
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tools:
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python: "mambaforge-latest"
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jobs:
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create_environment:
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- conda env create -p .env/ --file environment-files/readthedocs.yml
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build:
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html:
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#- PATH=$(pwd)/.env/bin/:$PATH q2doc refresh-cache
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- PATH=$(pwd)/.env/bin/:$PATH make html
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- mkdir -p $READTHEDOCS_OUTPUT
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- cp -a book/_build/* $READTHEDOCS_OUTPUT/
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conda:
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environment: environment-files/readthedocs.yml

‎Makefile‎

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# helpers
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_copy-env-file:
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cp environment-files/readthedocs.yml book/_static/environment.yml
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_copy-data:
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@if [ -d "book/data/" ]; then \
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cp -r book/data/ book/_build/html/data/; \
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echo "Copied data directory."; \
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else \
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echo "book/data/ not found, skipping copy."; \
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fi
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_build-html:
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cd book && jupyter book build --html
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_build-fast-preview:
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cd book && Q2DOC_FASTMODE= jupyter book build --html
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_build-preview:
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cd book && Q2DOC_PREVIEW= jupyter book build --html
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# main targets
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autodoc:
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q2doc autodoc --singlepage --plugin news.rachis.org --output plugin-reference book
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html: _copy-env-file _build-html _copy-data
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fast-preview: _copy-env-file _build-fast-preview _copy-data
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preview: _copy-env-file _build-preview _copy-data
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serve:
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npx serve book/_build/html/ -p 4000
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clean:
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rm -rf book/_build/html/

‎README.md‎

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# rachis project news source
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[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border-orange.json)](https://github.com/copier-org/copier)
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## Development instructions
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The following sub-sections illustrate how to develop this documentation.
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### Create the development environment
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To build this documentation locally for development purposes, first create your development environment.
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```
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cd news.rachis.org
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conda env create -n news.rachis.org --file environment-files/readthedocs.yml
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conda activate news.rachis.org
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q2doc refresh-cache
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```
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### Build the book
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Next, build the book:
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```
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make html
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```
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### Serve the book locally
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Finally, run the following to serve the built documentation locally:
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```
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make serve
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```
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Have fun!

‎book/_static/favicon.ico‎

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‎book/_static/logo-dark.png‎

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‎book/_static/logo-light.png‎

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‎book/intro.md‎

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# Introduction
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:::{tip} Are you in the right place?
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This is *rachis project news*, a collection of articles about the rachis project (formerly known as the QIIME 2 Framework).
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If you're looking to get started with QIIME 2, or for general information about the project, there are better resources.
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Are you looking for:
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- the QIIME 2 homepage? That's [https://qiime2.org](https://qiime2.org).
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- learning resources for microbiome marker gene (i.e., amplicon) analysis? See the [QIIME 2 *amplicon distribution* documentation](https://amplicon-docs.qiime2.org).
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- learning resources for microbiome metagenome analysis? See the [MOSHPIT documentation](https://moshpit.qiime2.org).
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- installation instructions, plugins, books, videos, workshops, or resources? See the [QIIME 2 Library](https://library.qiime2.org).
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- general help? See the [QIIME 2 Forum](https://forum.qiime2.org)
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- information about the author? See [https://cap-lab.bio](https://cap-lab.bio).
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Otherwise, if you're specifically looking for *rachis project news*, you're in the right place.
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[Read on... 📖](#tutorial)
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:::
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## License
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*rachis project news* (©2025) by [Greg Caporaso](https://cap-lab.bio) is licensed under [CC BY-NC-ND 4.0](https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en).

‎book/myst.yml‎

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# See docs at: https://mystmd.org/guide/frontmatter
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version: 1
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project:
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id: news.rachis.org
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title: rachis project news
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# description:
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keywords: ["QIIME", "QIIME 2", "microbiome", "metagenome"]
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# uncommenting "authors" will put the author list on every page
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# authors: ["Greg Caporaso"]
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# github:
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references:
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q2doc-api-target: https://develop.qiime2.org/en/latest/
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q2doc-usage-target: https://use.qiime2.org/en/latest/
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q2doc-library-target: https://library.qiime2.org
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q2doc-amplicon-target: https://amplicon-docs.readthedocs.io/en/latest/
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plugins:
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- type: executable
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path: q2doc-plug.py
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toc:
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- file: intro.md
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- file: tutorial.md
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- title: References
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children:
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- title: Plugin Reference
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children:
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- pattern: plugin-reference/plugins/*.md
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- title: Artifact Classes and Formats
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children:
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- pattern: plugin-reference/artifacts/*.md
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downloads:
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- file: _static/environment.yml
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title: Conda environment file
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site:
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template: https://github.com/ebolyen/myst-book-theme-poc.git
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options:
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folders: true
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favicon: _static/favicon.ico
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logo: _static/logo-light.png
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logo_dark: _static/logo-dark.png
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pretty_urls: false

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