New docker file + routine to create singularity image from Dockerfile

(works on my computer).

This allows me to more rapidly develp the Dockerfile. Also this commit
includes a separate conda environment which is going to be used within
singularity

docker/Dockerfile

+FROM rocker/r-ver:3.4.3
+
+MAINTAINER Sascha Meiers meiers@embl.de
+LABEL version="1.1"
+LABEL mosaicatcher_version="0.3.1-dev"
+# LABEL strandphaser_version="24eabf99a15c2ab959f7c5667cc22ef994cd0fc5"
+LABEL strandphaser_version="8011371c3a2f2d3a92116eb9df657b42d0b5e5b4"
+LABEL description="Required software dependencies for the MosaiCatcher pipeline (https://github.com/friendsofstrandseq/pipeline) to be used from within Snakemake."
+
+
+# Install basic required packages
+RUN apt-get update \
+    && 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 \
+        zlib1g-dev \
+        libbz2-dev \
+        liblzma-dev \
+        libxml2-dev \
+        gawk \
+        bcftools=1.3.1-1+b1 \
+        samtools=1.3.1-3 \
+    && apt-get autoremove -y \
+    && rm -rf /var/lib/apt/lists/* \
+    && ln -s $(which python3) /usr/local/sbin/python
+
+# Install basic R packages from a fixed R version (MRAN)
+RUN Rscript -e "install.packages(c( \
+        'assertthat', \
+        'dplyr', \
+        'data.table', \
+        'stringr', \
+        'ggplot2', \
+        'cowplot', \
+        'devtools', \
+        'reshape2', \
+        'doParallel', \
+        '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@8011371c3a2f2d3a92116eb9df657b42d0b5e5b4', dependencies = NA);" \
+    && rm -rf /usr/local/lib/R/site-library/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit
+
+# Install FreeBayes
+RUN apt-get update \
+    && BUILD_DEPS="git" \
+    && apt-get install --no-install-recommends -y $BUILD_DEPS \
+    && git clone --recursive git://github.com/ekg/freebayes.git \
+    && cd freebayes \
+    && make \
+    && cd \
+    && ln -s /freebayes/bin/freebayes /usr/local/sbin/freebayes \
+    && apt-get remove -y $BUILD_DEPS \
+    && apt-get autoremove -y \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install MosaiCatcher (and clean up afterwards)
+RUN apt-get update \
+    && BUILD_DEPS="cmake \
+        git" \
+    && apt-get install --no-install-recommends -y $BUILD_DEPS \
+    && git clone https://github.com/friendsofstrandseq/mosaicatcher.git \
+    && cd mosaicatcher \
+    && git checkout 0.3.1-dev \
+    && mkdir build \
+    && cd build \
+    && cmake ../src/ \
+    && cmake --build . \
+    && cd \
+    && ln -s /mosaicatcher/build/mosaic /usr/local/sbin/mosaic \
+    && apt-get remove -y $BUILD_DEPS \
+    && apt-get autoremove -y \
+    && rm -rf /var/lib/apt/lists/*
+
+
+# Install dependencies for python scripts
+ENV PATH="${PATH}:/miniconda/bin"
+RUN apt-get update \
+    && BUILD_DEPS="wget \
+        bzip2" \
+    && apt-get install --no-install-recommends -y $BUILD_DEPS \
+    && wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+    && chmod +x Miniconda3-latest-Linux-x86_64.sh \
+    && ./Miniconda3-latest-Linux-x86_64.sh -b -p /miniconda \
+    && rm -rf Miniconda3-latest-Linux-x86_64.sh \
+    && conda install \
+        scipy=1.1.0 \
+        pandas=0.23.4 \
+    && conda clean --all \
+    && apt-get remove -y $BUILD_DEPS \ 
+    && apt-get autoremove -y \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN conda create -n mosaic-env scipy=1.1.0 numpy=1.15.4 pandas=0.23.4
+

docker/def

+Bootstrap: docker
+Registry: http://localhost:5000
+Namespace: 
+From: mosaic:dev

docker/docker2singularity.sh

+#!/bin/bash
+imgname=mosaic
+
+echo "[d2s] Starting a local docker registry ..."
+docker run -d -p 5000:5000 --restart=always --name registry registry:2
+echo -e "\n"
+
+
+echo "[d2s] Build Docker image from Dockerfile ..."
+docker build -t ${imgname}:dev --network host .
+echo -e "\n"
+
+
+echo "[d2s] Tag newly build image to local registry ..."
+docker tag ${imgname}:dev localhost:5000/${imgname}
+echo -e "\n"
+
+
+echo "[d2s] Push newly build image to local registry ..."
+docker push localhost:5000/${imgname}
+echo -e "\n"
+
+
+echo "[d2s] Build singularity image file from Docker image ..."
+SINGULARITY_NOHTTPS=1 singularity build ${imgname}.simg docker://localhost:5000/${imgname}
+echo -e "\n"
+
+
+echo "[d2s] Stop local registry ..."
+docker container stop registry
+echo -e "\n"
+
+
+echo "[d2s] Remove registry container ..."
+docker container ls -aqf name=registry | xargs docker rm
+

docker/mosaic-env.yml

+name: mosaic
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - numpy=1.15.4
+  - pandas=0.23.4
+  - scipy=1.1.0