Updated rake for release

out/devel_mscore/Dockerfile

@@ -9,7 +9,7 @@ FROM bioconductor/devel_base2
 MAINTAINER lg390@cam.ac.uk
 
 RUN apt-get update -qq && \
-    apt-get install -y  --no-install-recommends \
+    apt-get install -y --no-install-recommends \
     libxt-dev libx11-dev libcairo2-dev \
     libfreetype6 \    
     libexpat1-dev \

out/release_base/Dockerfile

@@ -0,0 +1,52 @@
+# DO NOT EDIT FILES CALLED 'Dockerfile'; they are automatically
+# generated. Edit 'Dockerfile.in' and generate the 'Dockerfile'
+# with the 'rake' command.
+
+# The suggested name for this image is: bioconductor/release_base.
+
+FROM rocker/rstudio:3.5.3
+
+# FIXME? in release, default CRAN mirror is set to rstudio....should it be fhcrc?
+
+MAINTAINER maintainer@bioconductor.org
+
+# nuke cache dirs before installing pkgs; tip from Dirk E fixes broken img
+RUN  rm -f /var/lib/dpkg/available && rm -rf  /var/cache/apt/*
+
+
+# temporarily (?) change mirror used
+# RUN sed -i.bak 's!http://httpredir.debian.org/debian jessie main!http://mirrors.kernel.org/debian jessie main!' /etc/apt/sources.list
+
+# temporarily (?) remove explicit jessie source
+#RUN sed -i.bak -e '/deb http:..ftp.de.debian.org.debian jessie main/d' /etc/apt/sources.list
+
+# currently unstable option not available
+
+
+
+RUN apt-get update && \
+    apt-get -y  install --fix-missing gdb libxml2-dev python-pip libz-dev libmariadb-client-lgpl-dev
+    # valgrind
+
+
+RUN pip install awscli
+
+
+
+
+# requested install 
+RUN apt-get update && apt-get -y install libpng-dev
+
+# install headers needed for Rhtslib
+RUN apt-get update && apt-get -y install libbz2-dev liblzma-dev
+
+
+
+ADD install.R /tmp/
+
+RUN R -f /tmp/install.R
+
+RUN echo "R_LIBS=/usr/local/lib/R/host-site-library:\${R_LIBS}" > /usr/local/lib/R/etc/Renviron.site
+RUN echo "R_LIBS_USER=''" >> /usr/local/lib/R/etc/Renviron.site
+RUN echo "options(defaultPackages=c(getOption('defaultPackages'),'BiocManager'))" >> /usr/local/lib/R/etc/Rprofile.site
+