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diff --git a/paper-2026/README.md b/paper-2026/README.md new file mode 100644 index 0000000..3edc238 --- /dev/null +++ b/paper-2026/README.md @@ -0,0 +1,26 @@ +To replicate the results in the paper, please follow the instructions below. Guix is required. + +# Download data +Download https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/pggb/chroms/chr8.hprc-v1.0-pggb.gfa.gz and gunzip it. +``` +wget https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/pggb/chroms/chr8.hprc-v1.0-pggb.gfa.gz +gunzip chr8.hprc-v1.0-pggb.gfa.gz +``` + +# Install software +Drop into an environment with all the software installed. +``` +guix time-machine -C channels.scm -- shell -m manifest.scm +``` + +# Compile the ccwl workflow +Compile the ccwl workflow into CWL. +``` +ccwl compile benchmark.scm -o benchmark.cwl +``` + +# Run it +Run the CWL workflow using ravanan. If you need to add additional arguments so it runs on your HPC cluster, please do so. +``` +ravanan --guix-channels=channels.scm --store=store benchmark.cwl benchmark-inputs.yaml +``` |