QBiC Pipelines

This repository contains the documentation necessary to run different types of analysis in our clusters at QBIC.

Contributing to the documentation

To contribute to the documentation, please fork this repository and make a pull request to the dev branch. After review, please merge the PR. From time to time we will do merge to master and a documentation release.

Checking the documentation locally

To check locally how the documentation is building, you need to install the sphinx, recommonmark, sphinx-rtd-theme and httpserver dependencies. It requires Python 3!

pip install sphinx recommonmark httpserver sphinx-rtd-theme sphinx-markdown-tables

Then clone this repository from GitHub:

git clone git@github.com:qbic-pipelines/pipeline-docs.git

Go to the /docs directory of this repository and run:

make html

All the html files will be build under the _build directory. Then you can view the documentation in your browser by using the python built-in server:

python -m http.server

Go to the address shown in your browser, navigate to the _build directory and you can check out locally the documentation.

Deploying the documentation to readthedocs

This documentation is now hosted on readthedocs at: https://pipeline-docs.readthedocs.io. The documentation deployment is automated by changes to the GitHub repository.