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Dockerfile
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Dockerfile
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FROM rocker/r-ver:3.4
MAINTAINER Peter Kharchenko "peter_kharchenko@hms.harvard.edu"
RUN apt-get update --yes && apt-get install --no-install-recommends --yes \
build-essential \
cmake \
git \
libbamtools-dev \
libboost-dev \
libboost-iostreams-dev \
libboost-log-dev \
libboost-system-dev \
libboost-test-dev \
libssl-dev \
libcurl4-openssl-dev \
libxml2-dev \
libz-dev \
curl \
libhdf5-cpp-100 \
libarmadillo7 \
libarmadillo-dev
RUN \
R -e 'chooseCRANmirror(ind=52); install.packages(c("devtools", "Rcpp","RcppArmadillo", "Matrix", "mgcv", "abind","igraph","h5","Rtsne","cluster","data.table"))'
RUN \
R -e 'source("https://bioconductor.org/biocLite.R"); biocLite(c("pcaMethods","edgeR","Rsamtools","GenomicAlignments","GenomeInfoDb","Biostrings"),suppressAutoUpdate=TRUE,ask=FALSE,suppressUpdates=TRUE)'
RUN useradd -m user
USER user
ENTRYPOINT ["/bin/bash"]
WORKDIR "/home/user"
RUN \
git clone https://github.com/velocyto-team/velocyto.R && \
mkdir -p ~/R/x86_64-redhat-linux-gnu-library/3.4
RUN \
echo '.libPaths(c("~/R/x86_64-redhat-linux-gnu-library/3.4", .libPaths()))' > .Rprofile && \
R -e 'devtools::install_local("~/velocyto.R/",dep=T,upgrade_dependencies=F)'
ENV LD_LIBRARY_PATH=/usr/local/lib/R/lib/:$LD_LIBRARY_PATH \
R_PROFILE=~/.Rprofile