anchor.diff:      python-biopython \
       python-xlrd \
       python-openpyxl
  -RUN wget http://sf.net/projects/fusioncatcher/files/bootstrap.py -O bootstrap.py && python bootstrap.py -t --download -y
   
  -
  -#FusionInspector
  -RUN wget https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.4.0.tar.gz 
  -RUN make 
  -RUN make plugins
  +RUN wget http://sf.net/projects/fusioncatcher/files/bootstrap.py -O bootstrap.py && python bootstrap.py -t --download -y && rm bootstrap.py
   
   
   
  +#### STAR-Fusion START 
  +RUN apt-get update && apt-get install -y gcc g++ perl python automake make \
  +                                       wget curl libdb-dev \
  +                       bzip2 zlibc zlib1g zlib1g-dev  default-jre \
  +                       unzip && \
  +    apt-get clean
  +
  +RUN curl -L https://cpanmin.us | perl - App::cpanminus
  +## set up tool config and deployment area:
  +
  +ENV SRC /usr/local/src
  +ENV BIN /usr/local/bin
  +
  +ENV DATA /usr/local/data
  +RUN mkdir $DATA
  +
  +
  +## perl lib installations
  +
  +RUN cpanm install Set::IntervalTree  # now included w/ STAR-Fusion
  +RUN cpanm install DB_File
  +RUN cpanm install URI::Escape
  +RUN cpanm install Carp::Assert
  +RUN cpanm install JSON::XS.pm
  +
  +######################
  +## Tool installations:
  +######################
  +
  +
  +
  +########
  +# GMAP
  +
  +RUN GMAP_URL="http://research-pub.gene.com/gmap/src/gmap-gsnap-2017-01-14.tar.gz" && \
  +    cd $SRC && \
  +    wget $GMAP_URL && \
  +    tar xvf gmap-gsnap-2017-01-14.tar.gz && \
  +    cd gmap-2017-01-14 && ./configure && make && make install
  +
  +
  +ENV PERL5LIB ${STAR_FUSION_HOME}/PerlLib
  +
  +
  +
  +
  +
  +###############
  +## STAR-Fusion:
  +
  +ENV STAR_FUSION_VERSION=1.1.0
  +
  +RUN STAR_FUSION_URL="https://github.com/STAR-Fusion/STAR-Fusion/releases/download/v${STAR_FUSION_VERSION}/STAR-Fusion_v${STAR_FUSION_VERSION}.tar.gz" && \
  +    cd $SRC && \
  +    wget $STAR_FUSION_URL && \
  +    tar xvf STAR-Fusion_v${STAR_FUSION_VERSION}.tar.gz && \
  +    cd STAR-Fusion_v${STAR_FUSION_VERSION} && make
  +
  +ENV STAR_FUSION_HOME $SRC/STAR-Fusion_v${STAR_FUSION_VERSION}
  +
  +## FusionInspector now included with STAR-Fusion
  +
  +
  +########
  +# Samtools
  +
  +RUN SAMTOOLS_URL="https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2" && \
  +   cd $SRC && \
  +   wget $SAMTOOLS_URL && \
  +   tar xvf samtools-1.3.1.tar.bz2 && \
  +   cd samtools-1.3.1/htslib-1.3.1 && ./configure && make && make install && \
  +   cd ../ && ./configure --without-curses && make && make install
  +
  +
  +########
  +# Trinity
  +
  +ENV TRINITY_VERSION=2.4.0
  +
  +RUN TRINITY_URL="https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v${TRINITY_VERSION}.tar.gz" && \
  +   cd $SRC && \
  +   wget $TRINITY_URL && \
  +   tar xvf Trinity-v${TRINITY_VERSION}.tar.gz && \
  +   cd trinityrnaseq-Trinity-v${TRINITY_VERSION} && make
  +
  +
  +ENV TRINITY_HOME /usr/local/src/trinityrnaseq-Trinity-v${TRINITY_VERSION}
  +
  
positive.code: FROM openjdk:8
  
  LABEL authors="rickard.hammaren@scilifelab.se, phil.ewels@scilifelab.se" \
      description="Docker image containing all requirements for NGI-RNAfusion pipeline"
  
  
  
  #Fusioncatcher 
  RUN apt-get -y install \
      build-essential\
      libncurses5-dev \
  
negative.code:     gcc \
      g++ \
      bzip2 \
      cmake \
      automake \
      gzip \
  