50 lines
1.2 KiB
Docker
50 lines
1.2 KiB
Docker
FROM debian:bookworm-slim
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# Set environment variables
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ENV DEBIAN_FRONTEND=noninteractive
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# Install system dependencies
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RUN apt-get update -y && \
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apt-get install -y --no-install-recommends \
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wget \
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curl \
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aria2 \
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tar \
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gzip \
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gawk \
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bash \
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grep \
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procps \
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ca-certificates \
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libstdc++6 \
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libgomp1 \
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libatomic1 \
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zlib1g \
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libbz2-1.0 \
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&& rm -rf /var/lib/apt/lists/*
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# Create working directory
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WORKDIR /workspace
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# Download and install Foldseek binary
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RUN wget -q https://mmseqs.com/foldseek/foldseek-linux-avx2.tar.gz && \
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tar xzf foldseek-linux-avx2.tar.gz && \
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cp foldseek/bin/foldseek /usr/local/bin/foldseek && \
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chmod +x /usr/local/bin/foldseek && \
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rm -rf foldseek foldseek-linux-avx2.tar.gz
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# Create necessary directories
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RUN mkdir -p /workspace/input && \
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mkdir -p /workspace/output && \
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mkdir -p /workspace/databases && \
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mkdir -p /workspace/tmp
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# Set environment variables
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ENV PATH="/usr/local/bin:${PATH}"
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ENV TMPDIR="/workspace/tmp"
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# Create wrapper script
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RUN echo '#!/bin/bash\n\
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cd /workspace && foldseek "$@"' > /usr/local/bin/run_foldseek && \
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chmod +x /usr/local/bin/run_foldseek
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