This is the repo for the manuscript on SV genotyping using vg. The code to reproduce the analysis is available at https://github.com/vgteam/sv-genotyping-paper. Preprint versions are available on bioRxiv. It was published in Genome Biology on Feb 12 2020.
Quick "how to use":
- Write content in the Markdown files in the
- Write one-sentence per line (to get cleaner git diffs).
- E.g. citation:
[@tag:vgnbt]in with tag defined in
content/citation-tags.tsv. If it's a preprint from bioRxiv or it has a consortium name as an author it's safer to use
- Update title/author infos in content/metadata.yaml.
- More in
- In-text comments using:
<!-- This is a comment -->or
[//]: # (This is a comment).
- Travis is setup to build HTML/PDF (see buttons above). Or build locally.
- A few more utilities in the Makefile.
Manubot documentation: automated scholarly manuscripts on GitHub
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.
An overview manuscript presents the benefits of collaborative writing with Manubot and its unique features.
The rootstock repository is a general purpose template for creating new Manubot instances, as detailed in
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:
contentcontains the manuscript source, which includes markdown files as well as inputs for citations and references. See
USAGE.mdfor more information.
outputcontains the outputs (generated files) from the manubot including the resulting manuscripts. You should not edit these files manually, because they will get overwritten.
webpageis a directory meant to be rendered as a static webpage for viewing the HTML manuscript.
buildcontains commands and tools for building the manuscript.
cicontains files necessary for deployment via continuous integration. For the CI configuration, see
# 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
webpage.py scripts upon content changes:
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 branch uses GitHub Pages to host the following URLs:
- HTML manuscript at https://jmonlong.github.io/manu-vgsv/
- PDF manuscript at https://jmonlong.github.io/manu-vgsv/manuscript.pdf
For continuous integration configuration details, see
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/jmonlong/manu-vgsv.
Since CC BY is not ideal for code and data, certain repository components are also released under the CC0 1.0 public domain dedication (
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.