Generate PDF for BioHackrXiv.org
We use pandoc with LaTeX templates to generate the PDF from markdown that can be submitted to https://biohackrxiv.org/. Note we also have plans for an online tool that can do same from http://biohackrxiv.genenetwork.org/.
Quick start
BioHackrXiv use pandoc flavored markdown. It is very simple. See
=> https://github.com/biohackrxiv/bhxiv-gen-pdf/blob/master/example/logic/paper.md
and the raw text version
=> https://raw.githubusercontent.com/biohackrxiv/bhxiv-gen-pdf/master/example/logic/paper.md
It can embed LaTeX because pandoc generates LaTeX from markdown as an intermediate step towards generating the final PDF.
The easiest start is to take the files in ./example/doc and modify them. Don't change the file names as they are used to generate the final paper. In fact, you can copy these files into your own git repo and continue from there.
We have a web interface that allows you to generate the PDF at
=> http://preview.biohackrxiv.org/
Paste in the base URL for your repo and the tool will find the paper.md.
Notes:
- Do not paste the path to the paper itself - only the base repo URL.
- One repo can not contain multiple paper.md's. It will pick the first one it finds.
- For biohackathons it pays to add a template repo people can template from, e.g
=> https://github.com/biohackrxiv/bhxiv-gen-pdf-template
Introduction
Here you find the required steps to run to code on your own. There is also a dockerized version.
If you find any bugs, please propose improvements via PRs. Thanks!
Prerequisites
- ruby
- pandoc
- pandoc-citeproc
- pdflatex
- biblatex
Confirmed versions of the library can be found in Dockerfile
Install
Clone this git repository and install the prerequisites listed above
Run
Generate the PDF with
./bin/gen-pdf [dir] [bioh]
where dir points to a directory where paper.md and paper.bib reside and bioh refers to the event. Example events (for a full list see ./bin/gen-pdf):
"Japan2019", "France2019", "Covid2020"
For example from the repository try
./bin/gen-pdf example/logic/ "Covid2020"
which will currently generate the paper as paper.pdf.
Run via Docker
Build docker container and run
docker build -t biohackrxiv/gen-pdf:local -f docker/Dockerfile .
docker run --rm -it -v $(pwd):/work -w /work biohackrxiv/gen-pdf:local gen-pdf /work/example/logic
Note that the current working directory of host machine is mounted on /work inside the container
Run via GNU Guix
The guix-deploy starts a Guix container which allows running the generator and tests.
Trouble shooting
If you are not using Docker or Guix you may need to explicitely add ruby
ruby bin/gen-pdf [dir]
Run tests
ruby -I lib test/test_generator.rb