Moved Dockerfile and included dependencies for Python scripts

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 \
-        python3 \
-        python3-scipy \
-        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/*

docker/Dockerfile

@@ -97,13 +97,8 @@ RUN apt-get update \
     && 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