Updated OS, image pushed to Dockerhub trinityCTAT/inferCNV:3 .

Former-commit-id: da8a084

docker/Dockerfile

@@ -1,43 +1,22 @@
 # Docker file for inferCNV
+FROM ubuntu:xenial
 
-FROM ubuntu:trusty
+RUN echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" | tee -a /etc/apt/sources.list && \
 MAINTAINER [email protected]
 
-######################
-## Environment
-######################
+gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9 && \
+gpg -a --export E084DAB9 | apt-key add -
 
-## Constants
-### Locations
-ENV SRC /usr/local/src
-
-######################
-## Dependencies and Tools
-######################
-##############
-## Helper tools
 RUN apt-get update && \
- apt-get install -y git libxml2-dev r-cran-xml libcurl4-openssl-dev wget
-
-# Install dependencies for r-base source build
-RUN apt-get build-dep -y r-base
-
-## Install R 3.2.1
-WORKDIR ${SRC}
-RUN wget https://cran.r-project.org/src/base/R-3/R-3.2.1.tar.gz && \
- apt-get install -y tcl tcl-dev tk-dev tk && \
- tar xf R-3.2.1.tar.gz
+apt-get -y install curl libssl-dev libcurl4-openssl-dev libxml2-dev r-base r-base-dev git
 
-WORKDIR ${SRC}/R-3.2.1
-RUN ./configure --prefix=/usr/local --enable-R-shlib --with-tcltk && \
- make && \
- make install
+RUN echo "options(repos = c(CRAN = \"https://cran.rstudio.com\"))" >.Rprofile && \
+echo "install.packages(c(\"devtools\",\"ape\",\"GMD\",\"RColorBrewer\",\"optparse\",\"logging\"), dependencies =TRUE)" > install_devtools.r && \
+echo "library(\"devtools\")" >> install_devtools.r && \
+echo "install_github(\"broadinstitute/inferCNV\")" >> install_devtools.r && \
+R --no-save < install_devtools.r
 
-# Install R libraries
-RUN echo "options(repos=\"http://cran.rstudio.com/\")" > ${SRC}/install_pkgs.R && \
- echo "install.packages(c(\"GMD\", \"ape\", \"RColorBrewer\", \"optparse\", \"logging\"), repos=\"http://cran.us.r-project.org\", dependencies=TRUE)" >> ${SRC}/install_pkgs.R && \
- Rscript ${SRC}/install_pkgs.R
+RUN git clone https://github.com/broadinstitute/inferCNV.git
+ENV PATH=${PATH}:/inferCNV/scripts
 
-# Pull in inferCNV source
-WORKDIR ${SRC}
-RUN git clone https://github.com/broadinstitute/inferCNV
+CMD inferCNV.R --help