scripts/pan_skin/run_all.sh

#!/usr/bin/env bash
PANDA_ROOT="${PANDA_ROOT:-$(cd "$(dirname "${BASH_SOURCE[0]}")/../.." && pwd)}"
# canonical end-to-end pipeline
set -euo pipefail
cd "$PANDA_ROOT"
mkdir -p logs/pan_skin
LDLIBS=$(python -c "import site,os; print(os.path.join(site.getsitepackages()[0],'nvidia','cusparselt','lib'))" 2>/dev/null || echo "")
export LD_LIBRARY_PATH="$LDLIBS:${LD_LIBRARY_PATH:-}"
run() { echo "==== $1 ===="; python -u "$2" 2>&1 | tail -10; }

bash scripts/pan_skin/01_download_tier_a.sh > logs/pan_skin/01_download.log 2>&1
bash scripts/pan_skin/02_download_tier_b.sh > logs/pan_skin/02_download.log 2>&1
run 06_per_dataset   scripts/pan_skin/06_build_per_dataset_h5ads.py
run 07_hvg_pca       scripts/pan_skin/07_build_shared_hvgs_and_pca.py
run 08a_marker_labels scripts/pan_skin/08_assign_labels.py
run 08b_curated_override scripts/pan_skin/08b_curated_label_override.py
run 20_train         scripts/pan_skin/20_train_panda.py
run 30_zero_shot     scripts/pan_skin/30_zero_shot_aldrich.py
run 40_heldout_cv    scripts/pan_skin/40_heldout_5fold_cv.py
run 44_en1_cko       scripts/analysis/44_en1_cko_contrast.py
run 45_markers       scripts/analysis/45_marker_refinement.py
run 49_melanocyte    scripts/analysis/49_melanocyte_deep_dive.py
run 57_pathways      scripts/analysis/57_multiclass_pathway_analysis.py
echo "done"