mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-27 07:40:25 +08:00
63 lines
2.1 KiB
Plaintext
63 lines
2.1 KiB
Plaintext
FROM python:3.8.20-bullseye
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RUN apt-get update -y && apt-get upgrade -y && \
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apt-get install -y \
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git wget ncbi-blast+-legacy mafft build-essential vim unzip cmake gcc g++ \
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libomp-dev libboost-all-dev libeigen3-dev cpanminus && \
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rm -rf /var/lib/apt/lists/*
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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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# Guidance installation and debug for 'guidance.pl' file existence
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RUN git clone https://github.com/anzaika/guidance.git && \
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cd guidance && make
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# Guidance bio perl dependency
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RUN apt-get update && apt-get install -y cpanminus && \
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cpanm Bio::Perl
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# TrimAl installation
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RUN wget -O trimal-1.5.0.zip https://github.com/inab/trimal/archive/refs/tags/v1.5.0.zip && \
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unzip trimal-1.5.0.zip && \
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cd trimal-1.5.0/source && \
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make && \
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mkdir -p /usr/local/trimal && \
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cp trimal /usr/local/trimal/ && \
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ln -s /usr/local/trimal/trimal /usr/local/bin/trimal && \
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rm -rf /trimal-1.5.0.zip /trimal-1.5.0
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# Install FastTree
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RUN wget http://www.microbesonline.org/fasttree/FastTree && \
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chmod +x FastTree && \
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mv FastTree /usr/local/bin/
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# Clone IQ-TREE 2 repository and compile it
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RUN git clone --recursive https://github.com/iqtree/iqtree2.git && \
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cd iqtree2 && \
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git checkout v2.4.0 && \
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mkdir build && cd build && \
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cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ .. && \
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make -j$(nproc) && \
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make install && \
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cd ../.. && rm -rf iqtree2
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# Clean the container
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RUN rm -rf vsearch-2.21.0-linux-aarch64.tar.gz
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# EukPhylo installation
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RUN git clone -b Docker https://github.com/Katzlab/EukPhylo.git
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# Add executables to PATH
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ENV PATH="$PATH:/iqtree/bin/iqtree:/usr/local/vsearch/bin/vsearch:/usr/local/trimal/trimal:/usr/local/bin"
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# Change executable permissions on wrapper script
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RUN ["chmod", "+x", "/EukPhylo/PTL2/run_eukphylo.sh"]
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# Change executable permissions on guidance.pl after confirming its existence
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RUN ["chmod", "+x", "/guidance/www/Guidance/guidance.pl"]
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# Change entrypoint on execution of the container
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ENTRYPOINT ["bash", "/EukPhylo/PTL2/run_eukphylo.sh"]
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