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21b75e3 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 | #!/bin/bash
set -euo pipefail
ENCODER="${ENCODER:?must be set}"
REFERENCE_PARQUET="${REFERENCE_PARQUET:?must be set}"
READS="${READS:?must be set}"
REPO_URL="https://github.com/vedatonuryilmaz/dev_genopix.git"
REPO_BRANCH="${REPO_BRANCH:-ml-intern}"
DATA_DATASET="${DATA_DATASET:-vedatonuryilmaz/te-seqdata-v1}"
ARTIFACT_REPO="${ARTIFACT_REPO:?must be set}"
git clone --branch "$REPO_BRANCH" --depth 1 "$REPO_URL" deepgenopix
cd deepgenopix
uv sync --extra hf --extra quant
MODE=$([ "${RESUME:-0}" = "1" ] && echo resume || echo run)
QUANT_MODE="${QUANT_MODE:-snk_em}"
OUTPUT_NAME="${1:-$(uv run python scripts/run_names.py quantify --encoder "$ENCODER" --reads "$READS" --mode "$QUANT_MODE")}"
if [ "${RESUME:-0}" = "1" ]; then
uv run python scripts/hf_artifacts.py pull --repo "$ARTIFACT_REPO" --preset "$OUTPUT_NAME" --dest data/output
fi
uv run deepgenopix quantify \
--encoder "$ENCODER" \
--reference-parquet "$REFERENCE_PARQUET" \
--reads "$READS" \
--output-dir "data/output/$OUTPUT_NAME" \
--mode "$QUANT_MODE" \
--run-mode "$MODE" \
--json
uv run python scripts/hf_artifacts.py push --repo "$ARTIFACT_REPO" --preset "$OUTPUT_NAME" --source data/output
uv run python scripts/hf_artifacts.py push-quant \
--repo "$DATA_DATASET" \
--output-name "$OUTPUT_NAME" \
--quant-run-dir "data/output/$OUTPUT_NAME" \
--message "quant artifacts from $OUTPUT_NAME"
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