lelaboratoire / rethink-prs-ms

Manuscript for our MRS method
https://lelaboratoire.github.io/rethink-prs-ms/
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Automated scholarly manuscripts on GitHub

HTML Manuscript PDF Manuscript Build Status

Manuscript description

This repository includes the manuscript and analysis code for a current development of modification to the conventional calculation of Polygenic Risk Score (PRS). The manuscript is collaboratively written on GitHub using Manubot.

Manubot

Manubot is a system for writing scholarly manuscripts via GitHub. Manubot automates citations and references, versions manuscripts using git, and enables collaborative writing via GitHub. The rootstock repository is a general purpose template for creating new Manubot instances, as detailed in SETUP.md. See USAGE.md for documentation how to write a manuscript.

Please open an issue for questions related to Manubot usage, bug reports, or general inquiries.

Repository directories & files

The directories are as follows:

Local execution

To run the Manubot locally, install the conda environment as described in build. Then, you can build the manuscript on POSIX systems by running the following commands.

# Activate the manubot conda environment (assumes conda version >= 4.4)
conda activate manubot

# Build the manuscript, saving outputs to the output directory
sh build/build.sh

# At this point, the HTML & PDF outputs will have been created. The remaining
# commands are for serving the webpage to view the HTML manuscript locally.

# Configure the webpage directory
python build/webpage.py

# View the manuscript locally at http://localhost:8000/
cd webpage
python -m http.server

Sometimes it's helpful to monitor the content directory and automatically rebuild the manuscript when a change is detected. The following command, while running, will trigger both the build.sh and webpage.py scripts upon content changes:

sh build/autobuild.sh

Continuous Integration

Build Status

Whenever a pull request is opened, Travis CI will test whether the changes break the build process to generate a formatted manuscript. The build process aims to detect common errors, such as invalid citations. If your pull request build fails, see the Travis CI logs for the cause of failure and revise your pull request accordingly.

When a commit to the master branch occurs (for example, when a pull request is merged), Travis CI builds the manuscript and writes the results to the gh-pages and output branches. The gh-pages branch uses GitHub Pages to host the following URLs:

For continuous integration configuration details, see .travis.yml.

License

License: CC BY 4.0 License: CC0 1.0

Except when noted otherwise, the entirety of this repository is licensed under a CC BY 4.0 License (LICENSE.md), which allows reuse with attribution. Please attribute by linking to https://github.com/lelaboratoire/rethink-prs-ms.

Since CC BY is not ideal for code and data, certain repository components are also released under the CC0 1.0 public domain dedication (LICENSE-CC0.md). All files matched by the following glob patterns are dual licensed under CC BY 4.0 and CC0 1.0:

All other files are only available under CC BY 4.0, including:

Please open an issue for any question related to licensing.