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Pandoc

Pandoc is a versatile document conversion tool which can convert between numerous markup and word processing formats, including Markdown, HTML, LaTeX and PDF.

Pandoc is available as a module on Apocrita.

Pandoc is provided as a container

Pandoc requires a large number of packages which can only be practically installed inside a container. The pandoc command will work seamlessly on the cluster, however you can also access additional related packages installed in the container. This is demonstrated in the advanced example.

Pandoc is already bundled with R and RStudio, don't use the separate module

If you want to use Pandoc alongside R, then you shouldn't load the pandoc module separately. Pandoc is bundled with RStudio and should be automatically detected by R packages such as rmarkdown in any RStudio session. If you wish to use this bundled version with the R module, then you need to manually tell R where the RStudio Pandoc binary is using the following command (this example is for rmarkdown, other packages may need a different command):

rmarkdown::find_pandoc(dir = "/usr/lib/rstudio-server/bin/quarto/bin/tools/x86_64/")

Usage

To run the default installed version of Pandoc, simply load the pandoc module:

$ module load pandoc
$ pandoc --help
pandoc [OPTIONS] [FILES]
  -f FORMAT, -r FORMAT  --from=FORMAT, --read=FORMAT
  -t FORMAT, -w FORMAT  --to=FORMAT, --write=FORMAT
  -o FILE               --output=FILE
                        --data-dir=DIRECTORY
...(output has been truncated)

For full usage documentation, run pandoc --help or see the user guide.

Example of converting a markdown document to LaTeX with pandoc:

pandoc document.md -f markdown -t latex -s -o document.tex

Standalone option

When the -s/--standalone option is used, pandoc uses a template to add header and footer material that is needed for a valid self-standing document.

Example jobs

Serial jobs

Here are two example jobs each running on 1 core and 1GB memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load pandoc

# Convert markdown file to html
pandoc document.md -s -t html -o document.html

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load pandoc

# Convert LaTeX file to PDF
pandoc proposal.tex --from=latex --to=pdf -o proposal.pdf

Advanced example

The Apptainer container also has additional LaTeX packages required by Pandoc. To use these (for example, pdflatex), you need to call the commands from a container using apptainer, as below:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load pandoc

# Use pdflatex to create a pdf
apptainer exec $(which pandoc) \
  pdflatex latex-doc.tex

References