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Dockerfile
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FROM rocker/geospatial:4.1.1
MAINTAINER Naupaka Zimmerman "https://github.com/naupaka"
RUN apt-get update
RUN apt-get install -y openssh-server tmux nano git unzip \
bison byacc curl wget tar make gcc libz-dev shellcheck
##### bioawk #####
RUN mkdir -p /home/code/tools \
&& cd /home/code/tools; git clone https://github.com/lh3/bioawk.git \
&& cd /home/code/tools/bioawk; make
##### mothur #####
RUN curl -L https://github.com/mothur/mothur/releases/download/v1.39.5/Mothur.linux_64_static.zip -o /home/Mothur.linux_64_static.zip \
&& unzip /home/Mothur.linux_64_static.zip -d /home
###### R Packages ######
COPY . /home/rstudio/sfendos
WORKDIR /home/rstudio/sfendos
ENV RENV_VERSION 0.14.0
RUN R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"
RUN R -e "remotes::install_github('rstudio/renv@${RENV_VERSION}')"
RUN chown -R rstudio . \
&& sudo -u rstudio R -e 'renv::restore()'
##### Other misc #####
COPY init_docker.sh /
WORKDIR /home
RUN echo "export PATH=${PATH}:/home/code/tools/bioawk/:/home/mothur" >> /home/.profile
RUN echo "/usr/bin/bash" >> /home/.profile
CMD ["/usr/bin/bash", "/init_docker.sh"]
EXPOSE 8787