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FROM ubuntu:20.04
ENV DEBIAN_FRONTEND noninteractive
# Instal basic utilities
RUN apt-get update
RUN apt-get install -y --no-install-recommends git wget unzip bzip2 build-essential ca-certificates pip gnupg default-jdk
RUN apt-get update
## Add the antiSMASH debian repository
RUN apt-get install -y apt-transport-https
RUN wget http://dl.secondarymetabolites.org/antismash-stretch.list -O /etc/apt/sources.list.d/antismash.list
RUN wget -q -O- http://dl.secondarymetabolites.org/antismash.asc | apt-key add -
RUN apt-get update
## Install the binaries
RUN apt-get install -y hmmer2 hmmer diamond-aligner fasttree prodigal ncbi-blast+ muscle glimmerhmm meme-suite
RUN pip install Jinja2==3.0.1
## Install antiSMASH
RUN wget https://dl.secondarymetabolites.org/releases/6.1.1/antismash-6.1.1.tar.gz
RUN tar -zxf antismash-6.1.1.tar.gz
RUN pip install ./antismash-6.1.1
COPY proteins.dmnd /usr/local/lib/python3.8/dist-packages/antismash/databases/clusterblast/proteins.dmnd
RUN download-antismash-databases
RUN antismash --check-prereqs
# Install ARTS
## Install manual depencies
### trimal
RUN git clone https://github.com/inab/trimal.git \
&& cd trimal/source/ \
&& make \
&& cp trimal /usr/local/bin/ \
&& cd /
### mafft
RUN wget https://mafft.cbrc.jp/alignment/software/mafft_7.520-1_amd64.deb \
&& dpkg -i mafft_7.520-1_amd64.deb
### raxmlHPC
RUN git clone https://github.com/stamatak/standard-RAxML.git \
&& cd standard-RAxML/ \
&& make -f Makefile.SSE3.gcc \
&& cp ./raxmlHPC-SSE3 /usr/local/bin/ \
&& cd /
## Add related files
ADD . /arts/
WORKDIR /arts/
RUN mkdir /custom_files/
RUN mkdir /custom_reference/
## Install pip depencies
RUN pip install -r requirements.txt
RUN mv ranger-dtl-U /usr/local/bin/
# Cloning BiG-SCAPE
RUN git clone https://github.com/medema-group/BiG-SCAPE.git
# Install bigscape
RUN cd BiG-SCAPE \
&& wget https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz \
&& gunzip Pfam-A.hmm.gz \
&& hmmpress Pfam-A.hmm \
&& chmod +x /arts/BiG-SCAPE/*py \
&& chmod a+w /arts/BiG-SCAPE/domains_color_file.tsv \
&& chmod a+w /arts/BiG-SCAPE/Annotated_MIBiG_reference/
## Remove unnecessery files
RUN rm proteins.dmnd \
&& rm /antismash-6.1.1.tar.gz \
&& rm -r /trimal \
&& rm /mafft_7.520-1_amd64.deb \
&& rm -r /standard-RAxML \
&& rm -rf /var/lib/apt/lists/*
ENTRYPOINT ["python3", "artspipeline1.py"]