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| author | Arun Isaac | 2026-10-09 18:29:22 +0100 |
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| committer | Arun Isaac | 2026-10-09 18:29:22 +0100 |
| commit | d547fc8f78832698752fbf8fd75b57f482932a21 (patch) | |
| tree | b84f1df5c57395f92d76fd414cb6aef13994a663 /paper-2026/README.md | |
| parent | fd1982b4883e08710de42a972827bab48116b7f9 (diff) | |
| download | domagi-paper-2026-workflow.tar.gz domagi-paper-2026-workflow.tar.lz domagi-paper-2026-workflow.zip | |
Add paper workflow. HEAD paper-2026-workflow main
This workflow is used to compute the results in the paper.
Diffstat (limited to 'paper-2026/README.md')
| -rw-r--r-- | paper-2026/README.md | 26 |
1 files changed, 26 insertions, 0 deletions
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 +``` |
