Generate PDF for BioHackrXiv.org

This is a template for generating a BioHackrXiv publication for the Elixir Biohackathon 2022. The repository contains the information to generate a PDF on the command line.

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:

1. Do not paste the path to the paper itself - only the base repo URL.
2. One repo can not contain multiple paper.md's. It will pick the first one it finds.

Introduction

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]