anchor.diff:      gcc \
       g++ \
       bzip2 \
  -    make \
       cmake \
       automake \
       gzip \
  
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:     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 && 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}
  
  