Restructured Dockerfile to utilize layers. Also remove external data...

Restructured Dockerfile to utilize layers. Also remove external data (BSgenome.Hsapiens.UCSC.hg38) from image - this has to be provided by the user

Dockerfile

 FROM rocker/r-ver:3.4.3
 
 MAINTAINER Sascha Meiers meiers@embl.de
+LABEL version="1.0"
+LABEL mosaicatcher_version="develop"
+LABEL strandphaser_version="24eabf99a15c2ab959f7c5667cc22ef994cd0fc5"
+LABEL description="Required software dependencies for the MosaiCatcher pipeline (https://github.com/friendsofstrandseq/pipeline) to be used from within Snakemake."
 
 
-# Install MosaiCatcher (and clean up afterwards)
+# Install basic required packages
 RUN apt-get update \
-    && BUILD_DEPS="cmake \
-        git \
-        zlib1g-dev \
-        libxml2-dev" \
-    && apt-get install --no-install-recommends -y $BUILD_DEPS \
     && apt-get install --no-install-recommends -y \
         libssl-dev \
         libcurl4-openssl-dev \
@@ -25,47 +24,45 @@ RUN apt-get update \
         libboost-date-time1.62.0 \
         libboost-date-time1.62-dev \
         gawk \
-## Install samtools and Bcftools
-    && echo -e "\n\n########\nINSTALL SAMTOOLS/BCFTOOLS\n########\n" \
-    && apt-get install --no-install-recommends -y \
         bcftools=1.3.1-1+b1 \
         samtools=1.3.1-3 \
-## Install Mosaicatcher version
-    && echo -e "\n\n########\nINSTALL MOSAICATCHER\n########\n" \
-    && git clone https://github.com/friendsofstrandseq/mosaicatcher.git \
-    && cd mosaicatcher \
-    && git checkout develop \
-    && mkdir build \
-    && cd build \
-    && cmake ../src/ \
-    && cmake --build . \
-    && cd \
-    && ln -s /mosaicatcher/build/mosaic /usr/local/sbin/mosaic \
-## Install packages from a fixed version https://mran.microsoft.com/snapshot/2018-03-15
-    && echo -e "\n\n########\nINSTALL BASIC R PACKAGES\n########\n" \
-    && Rscript -e "install.packages(c( \
+    && apt-get autoremove -y \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install basic R packages from a fixed R version (MRAN)
+RUN Rscript -e "install.packages(c( \
         'assertthat', \
         'dplyr', \
         'data.table', \
         'stringr', \
         'ggplot2', \
         'cowplot', \
-        'devtools'))" \
-## Install StrandPhaseR & its many dependencies
-    && echo -e "\n\n########\nINSTALL STRANDPHASER + DEPENDENCIES\n########\n" \
-    && Rscript -e "install.packages(c( \
+        'devtools', \
         'reshape2', \
         'doParallel', \
-        'foreach')); \
-        source('http://bioconductor.org/biocLite.R'); \
+        'foreach'))"
+
+# Install StrandPhaseR
+RUN Rscript -e "source('http://bioconductor.org/biocLite.R'); \
         biocLite('BSgenome', ask=F); \
         biocLite('BSgenome.Hsapiens.UCSC.hg38', ask=F); \
         devtools::install_github('daewoooo/StrandPhaseR@24eabf99a15c2ab959f7c5667cc22ef994cd0fc5', dependencies = NA);" \
-## Clean up
-    && echo -e "\n\n########\nCLEAN UP\n########\n" \
-    && apt-get remove -y $BUILD_DEPS \
-    && apt-get autoremove -y \
-    && rm -rf /var/lib/apt/lists/*
-
+    && rm -rf /usr/local/lib/R/site-library/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit
 
+# Install MosaiCatcher (and clean up afterwards)
+RUN apt-get update \
+    && BUILD_DEPS="cmake \
+        git \
+        zlib1g-dev \
+        libxml2-dev" \
+    && apt-get install --no-install-recommends -y $BUILD_DEPS \
+    && git clone https://github.com/friendsofstrandseq/mosaicatcher.git \
+    && cd mosaicatcher \
+    && git checkout develop \
+    && mkdir build \
+    && cd build \
+    && cmake ../src/ \
+    && cmake --build . \
+    && cd \
+    && ln -s /mosaicatcher/build/mosaic /usr/local/sbin/mosaic \