mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-27 05:20:24 +08:00
54 lines
1.7 KiB
Plaintext
54 lines
1.7 KiB
Plaintext
# Base Image
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FROM python:3.8.20-bullseye
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# Install required system dependencies and clean up apt cache
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RUN apt-get update && apt-get install -y \
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wget \
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cmake \
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g++ \
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make \
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zlib1g-dev \
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libjemalloc-dev \
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unzip \
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git \
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ncbi-blast+ \
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&& rm -rf /var/lib/apt/lists/* # Clean apt cache to reduce image size
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# Install Python dependencies
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RUN pip install biopython==1.75 ete3==3.1.2 tqdm==4.66.4 six==1.17.0
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# Clone EukPhylo repository
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RUN git clone -b Docker https://github.com/Katzlab/EukPhylo.git
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# Install VSEARCH
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RUN wget https://github.com/torognes/vsearch/releases/download/v2.21.0/vsearch-2.21.0-linux-aarch64.tar.gz && \
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tar xzf vsearch-2.21.0-linux-aarch64.tar.gz && \
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mv vsearch-2.21.0-linux-aarch64 /usr/local/vsearch && \
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ln -s /usr/local/vsearch/bin/vsearch /usr/local/bin/vsearch && \
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rm -rf vsearch-2.21.0-linux-aarch64.tar.gz
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# Compile DIAMOND v2.1.11 from source
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RUN wget https://github.com/bbuchfink/diamond/archive/refs/tags/v2.1.11.tar.gz && \
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tar xzf v2.1.11.tar.gz && \
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cd diamond-2.1.11 && \
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mkdir build && cd build && \
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cmake .. && \
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make -j$(nproc) && \
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cp diamond /usr/local/bin/ && \
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cd ../.. && rm -rf diamond-2.1.11 v2.1.11.tar.gz
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# Verify DIAMOND installation
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RUN diamond --version
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# Verify installations
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RUN diamond --version && vsearch --version && blastn -version
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# Ensure executables are accessible
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ENV PATH="$PATH:/usr/local/vsearch/bin:/usr/local/bin"
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# Change executable permissions on wrapper script
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RUN chmod +x /EukPhylo/PTL1/Transcriptomes/Scripts/wrapper_submit.sh
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# Set container entrypoint
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ENTRYPOINT ["bash", "/EukPhylo/PTL1/Transcriptomes/Scripts/wrapper_submit.sh"]
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