Pipeline components for real-time phylodynamic analysis

Augur manuscript

Setup

conda create -n augur-manuscript graphviz pandoc
conda activate augur-manuscript

Compile manuscript

Use pandoc to compile the paper.

make

Alternately, use JOSS's Docker image to compile the paper from this paper directory.

docker run --rm \
    --volume $PWD:/data \
    --user $(id -u):$(id -g) \
    --env JOURNAL=joss \
    openjournals/paperdraft