Dockerfile

# vast-tools
# Usage: vast-tools [SUBCOMMAND]
FROM r-base:4.0.3
MAINTAINER Nuno Agostinho <nunodanielagostinho@gmail.com>

RUN apt-get update

RUN apt-get install -y bowtie
RUN apt-get install -y libcurl4-openssl-dev
RUN apt-get install -y libssl-dev
RUN apt-get install -y libssh2-1-dev
RUN apt-get install -y perl
RUN apt-get install -y libgit2-dev
RUN apt-get install -y libxml2-dev

RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile
RUN Rscript -e "install.packages('optparse')"
RUN Rscript -e "install.packages('RColorBrewer')"
RUN Rscript -e "install.packages('reshape2')"
RUN Rscript -e "install.packages('ggplot2')"
RUN Rscript -e "install.packages('MASS')"
RUN Rscript -e "install.packages('shiny')"
RUN Rscript -e "install.packages('devtools')"
RUN Rscript -e "devtools::install_github('kcha/psiplot')"

ENV SW=/root/software/
RUN mkdir -p ${SW}
WORKDIR ${SW}
ENV vasttools=vast-tools
COPY ${vasttools} ${vasttools}

ENV PATH="${PATH}:${SW}/${vasttools}"
RUN locale-gen --purge en_US.UTF-8
RUN echo -e 'LANG="en_US.UTF-8"\nLANGUAGE="en_US:en"\n' > /etc/default/locale