| """Make `biotool` reachable from inside an agent's workspace. |
| |
| The harnesses this targets -- codex, Biomni, our own loop -- give the model a shell and |
| nothing else, so a tool is only usable if it is on PATH in the working directory. This |
| writes a small launcher rather than requiring an installed package, which keeps the |
| integration harness-agnostic: any agent that can run a command can reach the tools. |
| |
| The launcher pins the interpreter and the source paths, because an agent's shell inherits |
| whatever environment the harness happened to set, and the benchmark's own solver commonly |
| creates and activates its own conda environment mid-run. |
| """ |
|
|
| from __future__ import annotations |
|
|
| import os |
| import stat |
| from pathlib import Path |
|
|
| RESEARCH_ROOT = Path(__file__).resolve().parent.parent |
| DEFAULT_PYTHON = "/home/pengchx3/envs/genebench-sandbox/bin/python" |
| DEFAULT_C2S_SRC = "/home/pengchx3/text-dna/scdistill/repos/cell2sentence/src" |
|
|
| LAUNCHER = """#!/bin/bash |
| # Auto-generated by vera.install_tools. Runs the structured biological tools with a |
| # pinned interpreter, so an agent that switches conda environments mid-run keeps access. |
| export PYTHONPATH="{research}:${{PYTHONPATH:-}}" |
| export C2S_SRC="${{C2S_SRC:-{c2s}}}" |
| # The user's profile points every HF_* variable at a path this job may not be able to |
| # write; set them together or the override is silently ignored. |
| CACHE="${{VERA_CACHE:-{cache}}}" |
| mkdir -p "$CACHE" 2>/dev/null || true |
| export HF_HOME="$CACHE" HF_HUB_CACHE="$CACHE/hub" HUGGINGFACE_HUB_CACHE="$CACHE/hub" |
| export HF_DATASETS_CACHE="$CACHE/datasets" HF_ASSETS_CACHE="$CACHE/assets" |
| export CELLTYPIST_FOLDER="$CACHE/celltypist" |
| # The experimental arm is baked in at install time, not inherited. The agent runs inside |
| # a sandbox whose environment the harness does not fully control, so a variable that |
| # merely "should propagate" would leave the A/B silently measuring nothing -- the exact |
| # failure class this work is about. |
| export BIOTOOL_CONFIDENT="{confident}" |
| exec "{python}" -m vera.biotool "$@" |
| """ |
|
|
| PROMPT = """A `biotool` command is available in your working directory. It gives you |
| structured biological tools and pretrained models that the shell alone does not: |
| |
| ./biotool list show every available tool and model |
| ./biotool call <name> '<json args>' gene, sequence, pathway and structure annotation |
| ./biotool taxonomy --fasta F identify the source organism of sequences by BLAST |
| ./biotool celltype --matrix DIR cell-type composition from expression, using two |
| independent models, with species auto-detected |
| ./biotool references reference genomes already staged and indexed here |
| ./biotool align --fastq F align a read sample and report the top loci |
| ./biotool breakpoints --fastq R1 R2 align the full library and report, at base |
| resolution, where reads stop matching the |
| reference: cut sites, fusion junctions, |
| integration sites, structural breakpoints |
| ./biotool variants --fastq R1 R2 substitutions the reads support, each with its |
| --region chr:a-b depth and allele fraction, ranked by support |
| |
| The references listed by `./biotool references` are already indexed, so `breakpoints` |
| skips the download and the index build. |
| |
| `breakpoints` reports positions to the base and `variants` reports allele fractions |
| against the depth actually observed; both are covered by tests, so prefer them over a |
| hand-written pileup when a coordinate or a variant call has to be exact. |
| |
| Both report a `competence` field. When it says INCONCLUSIVE the tool is telling you the |
| evidence does not separate the candidates, and the remaining work is yours -- not that |
| the top row is the answer. |
| |
| Dataset, accession and literature lookups are deliberately absent: this benchmark requires |
| you to solve the problem from the data you were given, and tools that would identify the |
| source study are blocked.""" |
|
|
|
|
| def install(workspace: Path, python: str = DEFAULT_PYTHON, |
| c2s_src: str = DEFAULT_C2S_SRC, cache: str | None = None, |
| confident: bool = False) -> Path: |
| """Write an executable `biotool` launcher into `workspace`. |
| |
| Args: |
| workspace: The agent's working directory. |
| python: Interpreter that has the dependencies. Pinned rather than inherited. |
| c2s_src: Vendored Cell2Sentence source. |
| cache: Writable cache root for model downloads. |
| confident: Select the CONFIDENT arm, in which tools report findings alone as |
| conventional tool APIs do. The default reports blind spots as well. Written |
| into the launcher rather than inherited, so the arm is a property of the |
| installed workspace and can be verified by reading it. |
| |
| Returns: |
| Path to the launcher. |
| """ |
| cache = cache or os.environ.get( |
| "VERA_CACHE", "/tmp/galaxy_srv_disk00/pengchx3/hf_biotool") |
| target = Path(workspace) / "biotool" |
| target.write_text(LAUNCHER.format(research=RESEARCH_ROOT, python=python, |
| c2s=c2s_src, cache=cache, |
| confident="1" if confident else "0")) |
| target.chmod(target.stat().st_mode | stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH) |
| return target |
|
|
