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FROM conda/miniconda3
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RUN apt-get update && apt-get install -y git wget
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SHELL ["/bin/bash", "-c"]
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WORKDIR /usr/src

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# Cloning BiG-SCAPE
RUN git clone https://git.wur.nl/medema-group/BiG-SCAPE.git
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# Create conda environment
RUN conda env create -f /usr/src/BiG-SCAPE/environment.yml
RUN echo "source activate bigscape" > ~/.bashrc
ENV PATH /usr/local/envs/bigscape/bin:$PATH
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ENV PATH /usr/src/BiG-SCAPE:$PATH
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RUN cd BiG-SCAPE \
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 && wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam34.0/Pfam-A.hmm.gz \
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 && gunzip Pfam-A.hmm.gz \
 && source activate bigscape \
 && hmmpress Pfam-A.hmm \
 && chmod +x /usr/src/BiG-SCAPE/*py \
 && chmod a+w /usr/src/BiG-SCAPE/domains_color_file.tsv \
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 && chmod a+w /usr/src/BiG-SCAPE/Annotated_MIBiG_reference/ \
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 && chmod 777 /home

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USER 1000:1000
RUN mkdir /home/input /home/output
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WORKDIR /home
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ENV LANG C.UTF-8
ENV LC_ALL C.UTF-8
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ENTRYPOINT ["bigscape.py"]
CMD ["--help"]