hotwa
ae4c6351d9
- Add pixi.toml with digger and pipeline environments - Implement PixiRunner class replacing DockerContainerManager - Add run_digger_stage.py for standalone digger execution - Update run_single_fna_pipeline.py to use PixiRunner - Remove docker dependency from pyproject.toml - Delete docker_client.py (no longer needed) BREAKING CHANGE: Docker is no longer required. Use 'pixi install' instead.
44 lines
1.1 KiB
TOML
44 lines
1.1 KiB
TOML
[workspace]
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name = "bttoxin-pipeline"
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channels = ["conda-forge", "bioconda", "bioconda/label/cf201901"]
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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.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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# 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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# =========================
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# pixi tasks
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# =========================
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[feature.pipeline.tasks]
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# 完整 pipeline（三阶段）
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pipeline = "python scripts/run_single_fna_pipeline.py"
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# 单独阶段
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digger-only = "python scripts/run_digger_stage.py"
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shotter = "python scripts/bttoxin_shoter.py"
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plot = "python scripts/plot_shotter.py"
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