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added Dockerfile #39

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2461100
add dockerfile
soymintc Jul 12, 2023
eeb49fe
add optparse
soymintc Jul 12, 2023
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27 changes: 27 additions & 0 deletions Dockerfile
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Original file line number Diff line number Diff line change
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# docker build -t shahcompbio/shatterseek .
# docker push shahcompbio/shatterseek

FROM rocker/r-ver:4.3.1

RUN apt-get update

# for R install
RUN apt-get install -y libcurl4-openssl-dev libssl-dev libssh2-1-dev libxml2-dev zlib1g-dev curl git

# R install
RUN apt-get install -y libbz2-dev liblzma-dev
RUN R -e "install.packages(c('devtools'))"
RUN R -e "install.packages(c('BiocManager'))"
RUN R -e "install.packages(c('MASS'))"
RUN R -e "install.packages(c('argparse'))"
RUN R -e "install.packages(c('tidyverse'))"
RUN R -e "install.packages(c('gridExtra'))"
RUN R -e "BiocManager::install('BiocGenerics')"
RUN R -e "BiocManager::install('graph')"
RUN R -e "BiocManager::install('S4Vectors')"
RUN R -e "BiocManager::install('GenomicRanges')"
RUN R -e "BiocManager::install('IRanges')"

RUN R -e "devtools::install_github('parklab/ShatterSeek')"

RUN R -e "install.packages(c('optparse'))"