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FROM ubuntu:18.04 as app
ARG DEBIAN_FRONTEND=noninteractive
RUN mkdir ~/.gnupg && echo "disable-ipv6" >> ~/.gnupg/dirmngr.conf \
&& apt update \
&& apt install -y -q apt-transport-https software-properties-common \
&& apt-key adv --homedir ~/.gnupg --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \
&& apt update \
&& add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/' \
&& apt install -y -q \
curl \
perl \
r-base \
gcc \
build-essential \
libx11-dev \
&& rm -rf /var/lib/apt/lists/*
# Install BLAST
RUN mkdir -p /tmp/blast \
&& mkdir /opt/blast \
&& curl ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.9.0/ncbi-blast-2.9.0+-x64-linux.tar.gz \
| tar -zxC /tmp/blast --strip-components=1 \
&& cd /tmp/blast/bin \
&& mv blastn makeblastdb blastp /opt/blast/ \
&& cd .. \
&& rm -rf /tmp/blast
ENV PATH /opt/blast:$PATH
# Install BEDTools
RUN curl -L -O -J https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools \
&& chmod +x bedtools \
&& mv bedtools /usr/local/bin/
# Install R dependencies
COPY install_r_dependencies.R /install_r_dependencies.R
RUN Rscript /install_r_dependencies.R \
&& rm -f /install_r_dependencies.R
RUN curl -L -O -J https://cran.r-project.org/src/contrib/Archive/randomForest/randomForest_4.6-14.tar.gz \
&& R CMD INSTALL randomForest_4.6-14.tar.gz \
&& rm -rf randomForest_4.6-14.tar.gz
# Install Clustal Omega
RUN curl -L -O -J http://www.clustal.org/omega/clustalo-1.2.4-Ubuntu-x86_64 \
&& mv clustalo-1.2.4-Ubuntu-x86_64 clustalo \
&& chmod +x clustalo \
&& mv clustalo /usr/local/bin/
# Install CPAN dependencies
RUN cpan App::cpanminus \
&& cpan JSON
# Copy in scripts & libs
RUN mkdir -p /predictor/SPN_Reference_DB
RUN mkdir -p /predictor/bLactam_MIC_Rscripts
COPY SPN_Reference_DB/ /predictor/SPN_Reference_DB/
COPY bLactam_MIC_Rscripts /predictor/bLactam_MIC_Rscripts/
COPY ExtractGene.pl /predictor/
COPY PBP-Gene_Typer.pl /predictor/
COPY pw_wrapper.sh /predictor/
COPY to_json.pl /predictor/
COPY transeq.pl /predictor/
COPY spn_pbp_amr /predictor/
RUN cd /predictor \
&& chmod +x *.sh \
&& chmod +x *.pl \
&& chmod +x spn_pbp_amr
ENV PATH /predictor:$PATH
ENV PATH /predictor/bLactam_MIC_Rscripts/:$PATH
# new base for testing
FROM app as test
RUN mkdir -p /test_data
COPY test_data /test_data
RUN spn_pbp_amr /test_data/contigs.fasta > result.json
RUN apt update && apt install -y -q jq
RUN jq --sort-keys . result.json > sorted_result.json && jq --sort-keys . /test_data/expected_result.json > sorted_expected_result.json
RUN cmp sorted_result.json sorted_expected_result.json