Olamide Isreal
42d4e6cb87
- Add Nextflow pipeline (main.nf) with Harbor container image - Add nextflow.config with k8s/k8s_gpu/standard profiles - Add params.json for TRS/WES parameter discovery - Add Dockerfile, entrypoint.py, meta.yml from original implementation - Update paths to use /omic/eureka/Pocketminer/ convention - Update .gitignore to allow params.json
38 lines
1.1 KiB
Docker
38 lines
1.1 KiB
Docker
FROM continuumio/miniconda3:latest
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ARG DEBIAN_FRONTEND=noninteractive
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# Update and install basic dependencies
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RUN apt-get update -y \
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&& apt-get -y upgrade --fix-missing \
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&& apt-get -y install git procps coreutils wget \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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WORKDIR /workspace
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# Clone PocketMiner repository
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RUN git clone https://github.com/Mickdub/gvp.git \
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&& cd gvp \
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&& git checkout pocket_pred
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# Create conda environment and install dependencies
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RUN conda create -n pocketminer python=3.9 -y && \
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conda install -n pocketminer -c conda-forge \
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numpy scipy pandas tensorflow tqdm mdtraj pyyaml -y && \
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conda clean -afy
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# Activate environment and set up PATH
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ENV PATH=/opt/conda/envs/pocketminer/bin:$PATH
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ENV CONDA_DEFAULT_ENV=pocketminer
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# Copy entrypoint script
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COPY entrypoint.py /workspace/entrypoint.py
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RUN chmod +x /workspace/entrypoint.py
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# Set Python path to include the gvp/src directory
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ENV PYTHONPATH=/workspace/gvp/src:$PYTHONPATH
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# Default command
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CMD ["python", "/workspace/entrypoint.py", "--help"]
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