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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/.

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 Dokerfile

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]