anchor.diff:  WORKDIR data/
   
   CMD bash
  +
  +
  +WORKDIR data/
  +
  +CMD bash
  
positive.code: 
  # Copy nvBowtie and nvBWT executables to /usr/local/bin/
  
  COPY /home/anton/nvbio/build/nvBowtie/nvBowtie/ /usr/local/bin/
  COPY /home/anton/nvbio/build/nvBWT/nvBWT/ /usr/local/bin/
  
  
  # Get SRA Tooklit from NCBI
  
  RUN wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.8.2-1/sratoolkit.2.8.2-1-ubuntu64.tar.gz && \
  		tar -zxf sratoolkit.2.8.1-2-ubuntu64.tar.gz && \
  		rm sratoolkit.2.8.1-2-ubuntu64.tar.gz
  ENV PATH $PATH:/sratoolkit.2.8.1-2-ubuntu64/bin
  
  
  # Get HaSAPPy from github --------------!!-- NEED TO ADD RefSeq_human_GRCh38-hg38.txt to /HaSAPPy/docs/
  
  RUN cd / && \
  		git clone https://github.com/gdiminin/HaSAPPy.git && \
  		HaSAPPy/program && \
  		chmod +x PreprocessReads
  
  # Generate annotation databases
  RUN python GeneReference_built.py -i /HaSAPPy/docs/mm10_REFSEQgenes.txt -o /HaSAPPy/docs/GeneReference_Mouse-MM10.pkl
  RUN python GeneReference_built.py -i  /HaSAPPy/docs/RefSeq_human_GRCh38-hg38.txt -o /HaSAPPy/docs/GeneReference_Homo.pkl
  
  
  # --------------- INIT -------------------------------
  
negative.code: LABEL source "HaSAPPy"
  
  # For nvidia-docker use:
  #		FROM nvidia/cuda:6.5-runtime-ubuntu14.04
  
  RUN apt-get update && apt-get install -y --no-install-recommends \
  		ubuntu-desktop \
  