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Dockerfile
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# docker build --no-cache -t singjust/dialignr:2.0.0 .
# docker push singjust/dialignr:2.0.0
FROM rocker/r-ver:4.1.0
#######################
## System
#######################
RUN apt-get update && \
apt-get install -y zlib1g-dev && \
apt-get install -y libcurl4-openssl-dev && \
apt-get install -y libssl-dev && \
apt-get install -y libnetcdf-dev && \
apt-get install -y libxml2-dev && \
apt-get install -y libglpk-dev && \
apt-get install -y libbz2-dev
RUN R -e "if(!requireNamespace('BiocManager', quietly = TRUE)){ install.packages('BiocManager')}; BiocManager::install('DIAlignR')"
#RUN R -e "if(!requireNamespace('devtools', quietly = TRUE)){ install.packages('devtools')}; devtools::install_github('singjc/DIAlignR', ref='feature/docker')"
RUN R -e "if (!requireNamespace('BiocManager', quietly = TRUE)){ install.packages('BiocManager')}; BiocManager::install('BiocParallel')"
RUN R -e "if(!requireNamespace('devtools', quietly = TRUE)){ install.packages('devtools')}; devtools::install_github('omegahat/Rcompression')"
COPY Rscript/alignTargetedRuns_cli.R /alignTargetedRuns_cli.R
ENTRYPOINT ["Rscript", "alignTargetedRuns_cli.R"]
CMD ["--help"]