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/.
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!
- ruby
- pandoc
- pandoc-citeproc
- pdflatex
- biblatex
Confirmed versions of the library can be found in Dokerfile
Clone this git repository and install the prerequisites listed above
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.
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
The guix-deploy starts a Guix container which allows running the generator and tests.
If you are not using Docker or Guix you may need to explicitely add ruby
ruby bin/gen-pdf [dir]