forked from FredHutch/Oncoscape
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Dockerfile
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Dockerfile
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# Use Ubuntu 14.04 as the base container
FROM ubuntu:14.04
MAINTAINER "Robert McDermott" robert.c.mcdermott@gmail.com
# ADD the CRAN Repo to the apt sources list
RUN echo "deb http://cran.fhcrc.org/bin/linux/ubuntu trusty/" > /etc/apt/sources.list.d/cran.fhcrc.org.list
# Add the package verification key
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 51716619E084DAB9
# Update the system and install packages
RUN apt-get -y update && apt-get -y install \
r-base=3.2.2* \
vim \
make \
m4 \
gcc \
g++ \
libxml2 \
libxml2-dev \
python-pip && \
pip install websocket-client
# create the sttrweb user and data directory
RUN useradd -u 7534 -m -d /home/sttrweb -c "sttr web application" sttrweb && \
mkdir /home/sttrweb/data && \
mkdir /home/sttrweb/Oncoscape && \
mkdir /home/sttrweb/rlib
# Set environment variable for Oncoscape data location
ENV ONCOSCAPE_USER_DATA_STORE file:///home/sttrweb/data
ENV R_LIBS /home/sttrweb/rlib
ADD Oncoscape /home/sttrweb/Oncoscape/Oncoscape
ADD analysisPackages /home/sttrweb/Oncoscape/analysisPackages
ADD dataPackages /home/sttrweb/Oncoscape/dataPackages
ADD installBioconductorPackages.R /home/sttrweb/Oncoscape/
ADD installRpackages_global.sh /home/sttrweb/Oncoscape/
ADD installRpackages_local.sh /home/sttrweb/Oncoscape/
ADD testAllWebsocketOperations.py /home/sttrweb/Oncoscape/
ADD makefile /home/sttrweb/Oncoscape/
WORKDIR /home/sttrweb/Oncoscape
RUN make install
RUN chown -R sttrweb:sttrweb /home/sttrweb
EXPOSE 7777
USER sttrweb
CMD export R_LIBS=/home/sttrweb/rlib && make oncoDocker