963215de2d
- Add filter to skip .zip and .tar.gz files when creating result archive - Update CRISPR feature with CASFinder dependencies (hmmer, blast, vmatch, etc.) - Add install-casfinder task for macsydata installation - Remove obsolete CRISPR test files Co-Authored-By: Claude <noreply@anthropic.com>
130 lines
3.4 KiB
TOML
130 lines
3.4 KiB
TOML
[workspace]
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name = "bttoxin-pipeline"
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channels = ["conda-forge", "bioconda"]
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platforms = ["linux-64"]
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version = "0.1.0"
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channel-priority = "disabled"
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# =========================
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# digger 环境：bioconda 依赖
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# =========================
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[feature.digger]
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channels = ["bioconda", "conda-forge", "bioconda/label/cf201901"]
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[feature.digger.dependencies]
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bttoxin_digger = "==1.0.10"
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perl = "==5.26.2"
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perl-file-tee = "==0.07"
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perl-list-util = "==1.38"
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blast = "==2.16.0"
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# =========================
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# pipeline 环境：Python 分析依赖
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# =========================
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[feature.pipeline.dependencies]
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python = ">=3.9"
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pandas = ">=2.0.0"
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matplotlib = ">=3.7.0"
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seaborn = ">=0.12.2"
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# =========================
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# frontend 环境：Node.js 前端依赖
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# =========================
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[feature.frontend.dependencies]
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nodejs = ">=20"
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pnpm = ">=10"
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# =========================
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# webbackend 环境：FastAPI 后端依赖
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# =========================
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[feature.webbackend.dependencies]
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python = ">=3.11"
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fastapi = "*"
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uvicorn = "*"
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sqlalchemy = "*"
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psycopg2 = "*"
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celery = "*"
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redis-py = "*"
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docker-py = "*"
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pydantic = "*"
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pydantic-settings = "*"
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python-dotenv = "*"
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httpx = "*"
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pytest = "*"
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# =========================
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# CRISPR-Cas 环境：预留用于未来的 CRISPR-Cas 分析
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# =========================
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# 此环境预留用于 CRISPR-Cas 系统分析模块
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# 实现计划：
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# 1. 使用 CRISPRCasFinder 或 similar 工具识别 CRISPR arrays
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# 2. 提取 spacer 序列并与毒素基因关联分析
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# 3. 评估 CRISPR-Cas 系统对宿主防御的影响
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#
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# 预期依赖（待激活时添加）:
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[feature.crispr.dependencies]
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python = ">=3.10"
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wget = "*"
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curl = "*"
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git = "*"
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java-jdk = "*"
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parallel = "*"
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perl-app-cpanminus = "*"
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hmmer = "*"
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emboss = "*"
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blast = "*"
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perl-bioperl-core = "*"
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perl-xml-simple = "*"
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perl-digest-md5 = "*"
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vmatch = "*"
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muscle = "*"
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prodigal = "*"
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mamba = "*"
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macsyfinder = "==2.1.2"
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[feature.crispr.tasks]
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install-casfinder = "macsydata install -u CASFinder==3.1.0"
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detect = "python tools/crispr_cas_analysis/scripts/detect_crispr.py"
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fusion = "python tools/crispr_cas_analysis/scripts/fusion_analysis.py"
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# =========================
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# 环境定义
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# =========================
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[environments]
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digger = ["digger"]
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pipeline = ["pipeline"]
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frontend = ["frontend"]
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webbackend = ["webbackend"]
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crispr = ["crispr"]
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# Actually, let's keep it simple. The tools are Python scripts. They can run in the 'pipeline' environment which has python and pandas.
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# The 'crispr' feature defines dependencies.
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# =========================
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# pipeline tasks
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# =========================
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[feature.pipeline.tasks]
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pipeline = "python scripts/run_single_fna_pipeline.py"
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digger-only = "python scripts/run_digger_stage.py"
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shoter = "python scripts/bttoxin_shoter.py"
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plot = "python scripts/plot_shotter.py"
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# =========================
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# frontend tasks
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# =========================
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[feature.frontend.tasks]
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fe-install = { cmd = "pnpm install", cwd = "frontend" }
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fe-dev = { cmd = "pnpm dev --host", cwd = "frontend" }
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fe-build = { cmd = "pnpm build", cwd = "frontend" }
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fe-test = { cmd = "pnpm test:unit --run", cwd = "frontend" }
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fe-lint = { cmd = "pnpm lint", cwd = "frontend" }
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# =========================
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# webbackend tasks
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# =========================
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[feature.webbackend.tasks]
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api-dev = "uvicorn backend.app.main:app --reload --host 0.0.0.0 --port 8000"
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api-test = "pytest backend/ -v"
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web-start = "bash scripts/start_web.sh"
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