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Dockerfile_for_pub
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FROM openanalytics/r-base
MAINTAINER Sonia Garcia-Ruiz "s.ruiz@ucl.ac.uk"
RUN apt-get update && apt-get install -y --no-install-recommends \
libxt-dev \
libcairo2-dev \
libxml2-dev \
libssl-dev \
libcurl4-openssl-dev \
#libv8-3.14-dev \ couldn't install this package. Instead installed the following. Solution from https://github.com/jeroen/V8/issues/49
libnode-dev \
#libsqlite3-dev \
#libmariadb-client-lgpl-dev \
python3.6 \
python3-pip \
python3-setuptools \
python3-dev \
&& rm -rf /var/lib/apt/lists/*
RUN apt-get update && apt-get install -y --no-install-recommends \
cmake \
libudunits2-dev \
libmariadbclient-dev \
#libmariadb-client-lgpl-dev \
libgeos-dev \
libgmp-dev \
libnlopt-dev
RUN mkdir /root/biotextquest_top2vec
COPY Rprofile.site /usr/lib/R/etc/
RUN pip install top2vec
#the following from https://www.r-bloggers.com/2021/05/dockerizing-shiny-applications/
RUN echo "local(options(shiny.port = 3838, shiny.host = '0.0.0.0'))" > /usr/lib/R/etc/Rprofile.site
RUN R -e 'install.packages("shinythemes", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("shinyWidgets", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("shinyBS", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("easyPubMed", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("text2vec", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("tokenizers", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("MCL", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("shinybusy", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("ggfortify", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("mongolite", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("shinyjs", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("SnowballC", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("udpipe", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("tidyr", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("emmeans", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("broom", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("httr", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("igraph", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("dplyr", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("stringr", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("quanteda.textstats", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("quanteda.textplots", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("quanteda", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("RMySQL", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("shinyjs", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("anytime", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("shinyWidgets", repos="http://cran.rstudio.com/", dependencies=T)'
RUN apt-get install -y --no-install-recommends libsasl2-dev
RUN R -e 'install.packages("mongolite", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("reticulate", repos="http://cran.rstudio.com/", dependencies=T)'
RUN R -e 'install.packages("rentrez", repos = "http://cran.rstudio.com/", dependencies=T)'
COPY ./biotextquest_for_pub/biotextquest_v4 /root/biotextquest_top2vec
EXPOSE 3838
CMD ["R", "-e", "shiny::runApp('/root/biotextquest_top2vec')"]