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# default R-version install via rocker, uses debian as a base
FROM rocker/r-ver:3.5.2
# install some likely used base unix dependencies
RUN apt-get update -qq && apt-get -y --no-install-recommends install \
libxml2-dev \
libxt-dev \
libjpeg-dev \
libglu1-mesa-dev \
libcairo2-dev \
libsqlite3-dev \
libmariadbd-dev \
libmariadb-client-lgpl-dev \
libpq-dev \
libmagick++-dev \
libssh2-1-dev \
libssl-dev \
libcurl4-openssl-dev \
libnss3 \
libclang-dev \
unixodbc-dev \
cargo \
wget \
bzip2 \
nano
# create some basic directories for binding ICB storages
RUN mkdir -p /storage/groups/ /storage/scratch/ /home/icb/johann.hawe/
# install some custom software
RUN mkdir /software/ && cd /software/
# install some basic packages
RUN install2.r --error \
--deps TRUE \
plyr \
dplyr \
knitr \
tidyverse \
DT \
data.table \
Rcpp
# also add some packages which just could be really useful
RUN R -e "source('https://bioconductor.org/biocLite.R')" \
-e "biocLite(c('feather', 'ggpubr', 'GenomicRanges', 'batchtools', 'mclust', 'mixR', 'mixtools'))"
RUN install2.r --error \
--deps TRUE \
devtools
# add custom packages
RUN R -e "source('https://bioconductor.org/biocLite.R')" \
-e "biocLite(c('BDgraph', 'GENIE3', 'GeneNet', 'Homo.sapiens', 'httr', 'Matrix', 'org.Hs.eg.db'))"
RUN R -e "source('https://bioconductor.org/biocLite.R')" \
-e "biocLite(c('pheatmap', 'preprocessCore', 'plsgenomics', 'qvalue', 'fdrtool', 'reshape2'))"
RUN R -e "source('https://bioconductor.org/biocLite.R')" \
-e "biocLite(c('RBGL', 'rtracklayer', 'scales', 'sva', 'illuminaHumanv3.db', 'FDb.InfiniumMethylation.hg19'))"
RUN R -e "source('https://bioconductor.org/biocLite.R')" \
-e "biocLite(c('AnnotationDbi', 'annotables', 'BSgenome.Hsapiens.UCSC.hg19'))"
RUN R -e "source('https://bioconductor.org/biocLite.R')" \
-e "biocLite(c('Rsamtools', 'Rgraphviz', 'cvTools', 'ROCR', 'doRNG'))"
RUN R -e "source('https://bioconductor.org/biocLite.R')" \
-e "biocLite(c('GSEABase', 'GOstats'))"
RUN R -e "source('https://bioconductor.org/biocLite.R')" \
-e "biocLite(c('glasso'))"
RUN mkdir /r-packages/
COPY iRafNet_1.1-2.tar.gz /r-packages/iRafNet_1.1-2.tar.gz
RUN R CMD INSTALL /r-packages/iRafNet_1.1-2.tar.gz
RUN R -e "source('https://bioconductor.org/biocLite.R')" \
-e "biocLite(c('huge'))"
RUN R -e "library(devtools)" \
-e "install_github('zdk123/SpiecEasi')"
RUN R -e "library(devtools)" \
-e "devtools::install_github('andreyshabalin/MatrixEQTL')"
RUN R -e "source('https://bioconductor.org/biocLite.R')" \
-e "biocLite(c('meta'))"
RUN R -e "source('https://bioconductor.org/biocLite.R')" \
-e "biocLite(c('mvtnorm'))"
# system clean up
RUN rm -rf /var/lib/apt/lists/* \
&& apt-get clean \
&& apt-get purge
# R cleanup
RUN rm -rf /tmp/downloaded_packages/ /tmp/*.rds