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Dockerfile-dev
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Dockerfile-dev
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FROM ubuntu:20.04
################## METADATA ######################
LABEL version="0.2"
LABEL software="GenomeChronicler"
LABEL about.tags="GenomeChronicler, PGP-UK"
LABEL description="Docker image containing base requirements for PGP-UK GenomeChronicler"
ENV LC_ALL=C
ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update \
&& apt-get install -y \
software-properties-common \
wget \
r-base-core \
tk-dev \
mesa-common-dev \
python3 python3-pip \
libhts-dev \
&& add-apt-repository ppa:linuxuprising/java \
&& apt-get install -y openjdk-8-jdk
# Python
RUN pip3 install fire==0.5.0 pandas==1.5.3 xlsxwriter==3.0.9 tqdm==4.65.0 \
matplotlib==3.7.1 seaborn==0.12.2
# R
RUN R --slave -e 'install.packages(c("RColorBrewer", "TeachingDemos"))'
# LaTeX - update needed for repos after R
RUN apt-get install -y \
texlive-latex-base \
texlive-fonts-recommended \
texlive-latex-extra \
lmodern \
&& apt-get clean \
&& apt-get purge \
&& rm -rf /var/lib/apt/lists/* /tmp/*
RUN wget https://github.com/samtools/htslib/releases/download/1.16/htslib-1.16.tar.bz2 \
&& tar -xjf htslib-1.16.tar.bz2 && rm htslib-1.16.tar.bz2 \
&& cd htslib-1.16 && ./configure && make && make install
RUN wget https://github.com/samtools/samtools/releases/download/1.16.1/samtools-1.16.1.tar.bz2 \
&& tar -xjf samtools-1.16.1.tar.bz2 && rm samtools-1.16.1.tar.bz2 \
&& cd samtools-1.16.1 && ./configure && make && make install
RUN wget https://github.com/samtools/bcftools/releases/download/1.16/bcftools-1.16.tar.bz2 \
&& tar -xjf bcftools-1.16.tar.bz2 && rm bcftools-1.16.tar.bz2 \
&& cd bcftools-1.16 && ./configure && make && make install
WORKDIR /GenomeChronicler
RUN wget -qO- https://github.com/PGP-UK/GenomeChronicler/releases/download/0.91/reference.tar.gz | tar xvz
RUN wget -qO- https://github.com/PGP-UK/GenomeChronicler/releases/download/0.91/software.tar.gz | tar xvz software.linux && mv software.linux software
ENV PATH "$PATH:/GenomeChronicler/scripts"
CMD /GenomeChronicler/scripts/genomechronicler