Morphic Recipes

Operational recipes for running STAR-suite on Morphic/JAX/MSK/UCSF datasets.

This repo is the transition target for dataset-specific launchers, downstream h5ad/QC/CellBender/celltyping helpers, workflow schemas, manifests, and handoff packet builders. STAR-suite remains the canonical home for core STAR/Flex/Solo source, compiled tools, core tests, release packaging, and generic MCP server code.

Status

Phase: Phase 1 cutover.

The first import was copied from STAR-suite commit:

43a5853af0c627925f827ab576814b770d1874c1

During the transition, files may exist in both repos. Treat this repo as the canonical home for production recipe work. STAR-suite compatibility launchers should delegate here while the duplicated scripts age out.

Layout

docs/                  Dataset runbooks and recipe-specific handoffs
docs/production_recipes/
                       Human-facing summaries for production recipe chains
scripts/               Production launchers and downstream helpers
mcp_server/workflows/  Mirrored workflow YAMLs during transition
config/                Local environment templates

Using Recipes

Production launchers that need STAR core tools default to the local core checkout at /mnt/pikachu/STAR-suite. Override that checkout with STAR_SUITE_ROOT when running from another host or clone:

export STAR_SUITE_ROOT=/mnt/pikachu/STAR-suite
--star-bin /mnt/pikachu/STAR-suite/core/legacy/source/STAR
--genome-dir /storage/autoindex_110_44/bulk_index

For CellBender production or handoff workflows, GPU mode is mandatory. The rendered command must include the recipe-level GPU flag, Docker GPU access, and CellBender --cuda.

STAR CLI MCP Recipes

The mirrored MCP workflow schemas under mcp_server/workflows/ expose operator-facing STAR commands during the repo split. The paired CBQ/BINSEQ batch recipe is star_binseq_pe_batch; STAR-Flex CBQ is star_flex_fixed_rna_cbq. Both render --readFilesType Binseq PE with no --readFilesCommand. See docs/RUNBOOK_STAR_BINSEQ_CBQ_BATCH.md.

The multiome lane recipe also accepts native CBQ on both sides: scripts/run_star_multiome_lane_smoke.sh --input-format cbq --gex-cbq ... plus --atac-read-pair-cbq ... --atac-barcode-cbq .... That path renders STAR GEX CBQ input and libchromap ATAC CBQ input without --readFilesCommand.

Canonical Boundary

• Core behavior, source changes, and core regression tests: STAR-suite.
• Dataset launch, remote staging, downstream analysis, and handoff packaging: this repo.
• Executed run records, exact commands, checksums, and environment pins: morphic-provenance.

See MIGRATION_INVENTORY.md for the initial file ownership classification.