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docs: Add tutorial for running SACCELERATOR with LSF/Mamba and new Xenium ovarian cancer datasets#356

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docs: Add tutorial for running SACCELERATOR with LSF/Mamba and new Xenium ovarian cancer datasets#356
Copilot wants to merge 2 commits into
nativefrom
copilot/tutorial-for-pipeline-usage

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Copilot AI commented May 31, 2026

Tutorial for running the pipeline on HPC with LSF (bsub) and Mamba, including how to manage Snakemake's hashed conda environments and how to add new datasets.

Contents (docs/tutorial_lsf_mamba.md)

  • Running on example datasets — Full walkthrough using libd_dlpfc and xenium-breast-cancer with an LSF Snakemake profile (covers both Snakemake 7.x and 8.x plugin-based configs)
  • Conda environment naming/reuse — Solutions for the hashed env directory problem:
    • --conda-prefix for shared persistent cache
    • Helper script to pre-create named envs (saccelerator_method_spaGCN, etc.)
    • --conda-create-envs-only for upfront env resolution
  • Adding new Xenium ovarian cancer datasets — Template data module (script, env YAML, optargs JSON, config entries) for:
    • Xenium Prime FFPE Human Ovarian Cancer
    • Xenium Comparison Fresh Frozen Human Ovarian Cancer

Example LSF profile snippet:

executor: lsf
jobs: 50
use-conda: true
conda-frontend: mamba
conda-prefix: /path/to/shared/conda_envs
default-resources:
  mem_mb: 8000
  runtime: 120
  lsf_queue: normal

Note: The download script templates require users to fill in actual 10x Genomics URLs (gated behind their ToS acceptance page).

Copilot AI changed the title docs: Add tutorial for running SACCELERATOR with LSF/Mamba on example and new Xenium ovarian cancer datasets docs: Add tutorial for running SACCELERATOR with LSF/Mamba and new Xenium ovarian cancer datasets May 31, 2026
Copilot AI requested a review from shwong-tw May 31, 2026 21:57
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