onlybelter/rpy2-docker repository overview

broom
DBI
dbplyr
dplyr
hexbin
ggplot2
lme4
RSQLite
tidyr
beeswarm
CHNOSZ
maptools
mailR
missForest
pbapply
princurve
pryr
randomForest
readr
readxl
rmarkdown
R.oo
tibble
zip
pheatmap
rJava

Rdisop
BiocParallel
ggplot2
graph
gridExtra
igraph
impute
snow

mysqlclient==1.3.12

FROM rpy2/rpy2:2.9.x

MAINTAINER Laurent Gautier <[email protected]>, Xin Xiong <[email protected]>

ARG DEBIAN_FRONTEND=noninteractive
ARG CRAN_MIRROR=https://cran.revolutionanalytics.com/

RUN \
  apt-get update -qq && \
  apt-get install -y \
                     software-properties-common\
                     python3-dev \
                     libssl-dev \
                     libcurl4-openssl-dev \
                     libxml2-dev

# install MariaDB
RUN \
  apt-key adv --recv-keys --keyserver hkp://keyserver.ubuntu.com:80 0xF1656F24C74CD1D8  &&\
  add-apt-repository 'deb [arch=amd64,i386,ppc64el] http://mirrors.neusoft.edu.cn/mariadb/repo/10.2/ubuntu xenial main' &&\
  apt-get update -qq && \
  apt-get install -y \
                     mariadb-client \
                     libmariadbclient-dev
# install Java
RUN \
  apt-get install -y openjdk-8-jdk  && \
  rm -rf /var/lib/apt/lists/*  && \
  R CMD javareconf

ADD ./package/ /src/
RUN \
  cd /src && \
  R -e 'install.packages(sub("(.+)\\\\n","\\1", scan("rpacks.txt", "character")), repos="'"${CRAN_MIRROR}"'")'
RUN \
  cd /src && \
  R -e 'source("http://bioconductor.org/biocLite.R"); biocLite(sub("(.+)\\\\n","\\1", scan("biocLite.txt", "character")))'

RUN \
  cd /src && \
  pip3 --no-cache-dir install -r requirements.txt && \
  rm -rf /root/.cache

ADD ./code/ /code/

RUN \
  apt-get update && \
  apt-get install -y pandoc