Add analysis/replicate.sh — single-command driver for the primary analysis#1
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ppavlidis wants to merge 1 commit into
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Add analysis/replicate.sh — single-command driver for the primary analysis#1ppavlidis wants to merge 1 commit into
ppavlidis wants to merge 1 commit into
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…lysis Mirrors the revisions/replicate.sh layout (phases + DRY_RUN + PHASES filter) but drives the original-submission pipeline under analysis/strains/ (00–04) and analysis/cell_lines/ (00–07), via the shared analysis/_downloads/ download. OPENAI_API_KEY is resolved from the macOS Keychain with ~/openai/access_key.txt and pre-set env var as fallbacks (inst/gpt.py already supports the file path). The 02 / 05 R scripts that issue OpenAI Batch jobs already block on completion via R/run_batches.R, so the bash driver does not need a poll loop of its own. Smoke-tested under DRY_RUN=1. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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Summary
Adds
analysis/replicate.sh, a single-command driver for the original-submission pipeline. It mirrors the layout ofrevisions/replicate.sh(phases,DRY_RUN,PHASESfilter, Keychain-based key resolution) but drives the scripts underanalysis/strains/(00–04) andanalysis/cell_lines/(00–07), preceded by the sharedanalysis/_downloads/download.R.keys→downloads→strains→cells.OPENAI_API_KEYresolves from the macOS Keychain, then a pre-set env var, then~/openai/access_key.txt(the existinginst/gpt.pyalready supports the file path).R/run_batches.R, so the bash driver does not need its own poll loop.revisions/replicate.shso the original and revision-round drivers do not drift.Test plan
DRY_RUN=1 ./analysis/replicate.shprints the full ordered command list across all four phases.data-raw/strain_data/main_frame.rdsanddata-raw/cell_line_data/cell_line_inputs_second_pass.rdsfrom a cold start.🤖 Generated with Claude Code