Here we run a simple R script that writes a data.frame to a TSV file, and
exports a ggplot2 plot to a PNG file. These files are subsequently copied to
the specified output GCS bucket.
cd examples/r
dataset="fewgenomes"
outdir="$(whoami)-test-r-1"
# make sure you've installed https://anaconda.org/cpg/analysis-runner
analysis-runner \
--access-level "test" \
--dataset ${dataset} \
--description "testing R" \
--output-dir ${outdir} \
--image australia-southeast1-docker.pkg.dev/analysis-runner/images/driver-r:1.2
script.R
# Check that the output GCS bucket contains the files:
gsutil ls gs://cpg-${dataset}-test-tmp/${outdir}