Add Dockerfile + singularity config

Dockerfile

+FROM rocker/r-ver:3.4.3
+
+MAINTAINER Sascha Meiers meiers@embl.de
+
+
+# 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 \
+    && apt-get install --no-install-recommends -y \
+        libssl-dev \
+        libcurl4-openssl-dev \
+        libboost-program-options1.62.0 \
+        libboost-program-options1.62-dev \
+        libboost-random1.62-dev \
+        libboost-system1.62.0 \
+        libboost-system1.62-dev \
+        libboost-filesystem1.62.0 \
+        libboost-filesystem1.62-dev \
+        libboost-iostreams1.62.0 \
+        libboost-iostreams1.62-dev \
+        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( \
+        '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( \
+        'reshape2', \
+        'doParallel', \
+        'foreach')); \
+        source('http://bioconductor.org/biocLite.R'); \
+        biocLite('BSgenome', 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/*
+
+
+

Snake.config-singularity.json

+{
+    "chromosomes"   : ["chrX","chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22"],
+
+
+    "reference"     : "/reference.fa",
+    "mosaicatcher"  : "mosaic",
+    "plot_script"   : "/mosaicatcher/R/qc.R",
+    "sv_plot_script": "/mosaicatcher/R/chrom.R",
+    "norm_script"   : "/mosaicatcher/R/norm.R",
+    "samtools"      : "samtools",
+    "bcftools"      : "bcftools",
+
+    "snv_calls"     : {},
+
+    "variable_bins" : {
+        "50000"     : "utils/variable_bins.GRCh38.50kb.bed",
+        "100000"    : "utils/variable_bins.GRCh38.100kb.bed"
+    },
+    "R_reference"   : "BSgenome.Hsapiens.UCSC.hg38",
+
+    "bp_density"    : {
+        "few"       : 0.2,
+        "medium"    : 0.4,
+        "many"      : 0.6
+    },
+
+    "paired_end"    : true,
+
+    "simulation_min_vaf" : 0.01,
+    "simulation_max_vaf" : 1.0,
+    "simulation_neg_binom_p" : {
+        "50000" : 0.4,
+        "100000" : 0.3,
+        "500000" : 0.1
+    },
+    "simulation_min_reads_per_library" :  500000,
+    "simulation_max_reads_per_library" : 1000000,
+    "simulation_window_sizes" : [50000, 100000],
+    "simulation_cell_count" : 100,
+    "simulation_alpha" : 0.02,
+
+    "genome_size" : 3e9
+
+}