anchor.diff:  
   
   ##########################################################################################
  -# ALEA 1.t.2
  +# ALEA2 2.0
   ##########################################################################################
   
   ENV ALEA_INSTALL_DIR=/opt/alea
  -ENV ALEA_VERSION=rt
  +ENV ALEA_VERSION=2.0
   ENV ALEA_FILENAME=alea.${ALEA_VERSION}.tar.gz
   #ENV ALEA_URL=https://github.com/hyounesy/ALEA/raw/Task/dist/${ALEA_FILENAME}
   #https://github.com/hyounesy/ALEA/raw/master/dist/alea.1.2.2.tar.gz
   
  -ENV ALEA_URL=https://datahub-7ak6xof0.udes.genap.ca/${ALEA_FILENAME}
  -
  -
  -WORKDIR /tmp
  -#COPY  ${ALEA_FILENAME} ${ALEA_FILENAME}
  -RUN wget -q $ALEA_URL && \
  -  tar -zxvf ${ALEA_FILENAME} -C /opt && \
  +ENV ALEA_URL=https://github.com/hyounesy/ALEA/raw/master/dist/${ALEA_FILENAME}
  +
  +
  +WORKDIR /tmp
  +COPY  ${ALEA_FILENAME} ${ALEA_FILENAME}
  +RUN wget -q $ALEA_URL
  +RUN  tar -zxvf ${ALEA_FILENAME} -C /opt && \
     rm -f /tmp/${ALEA_FILENAME}
   
   
  
positive.code: ##########################################################################################
  # Dockerfile
  #
  # Software:         ALEA
  # Software Version: alea.1.t.rt
  # Description:      A toolbox for Allele-specific Epigenomics Analysis
  # Base Image:       java:7
  # Build Cmd:        docker build -t taskkoike/alea:1.t.rt /path/to/dockerfile-directory/
  # Pull Cmd:         docker pull taskkoike/alea:1.t.rt
  # Run Cmd:          docker run -it taskkoike/alea:1.t.rt
  ##########################################################################################
  
  FROM java:7
  
negative.code:   ln -s /opt/shapeit/bin/shapeit $ALEA_INSTALL_DIR/bin/ && \
    find $VCFTOOLS_INSTALL_DIR/bin/ -maxdepth 1 -perm -+x -type f | xargs -i ln -s {} $ALEA_INSTALL_DIR/bin/ && \
    find /opt/bedtools2/bin/ -maxdepth 1 -perm -+x -type f | xargs -i ln -s {} $ALEA_INSTALL_DIR/bin/ && \
    find /opt/bedops/bin/ -maxdepth 1 -perm -+x -type f | xargs -i ln -s {} $ALEA_INSTALL_DIR/bin/ && \
    find /opt/bismark_v0.16.3/ -maxdepth 1 -perm -+x -type f | xargs -i ln -s {} $ALEA_INSTALL_DIR/bin/ && \
    find /opt/tophat-2.1.1.Linux_x86_64/ -maxdepth 1 -perm -+x -type f | xargs -i ln -s {} $ALEA_INSTALL_DIR/bin/ && \
    ln -s /opt/STAR-2.5.1b/source/STAR $ALEA_INSTALL_DIR/bin/
  
  #  find /opt/bedtools22/bedtools2/bin/ -maxdepth 1 -perm -+x -type f | xargs -i ln -s {} $ALEA_INSTALL_DIR/bin/bedtools22 && \
  
  RUN  find /opt/bowtie2-2.2.9/ -maxdepth 1 -perm -+x -type f | xargs -i ln -s {} /usr/local/bin/ 
  
  