anchor.diff:  LABEL source "HaSAPPy"
   
   # For nvidia-docker use:
  -#               FROM nvidia/cuda:6.5-runtime-ubuntu14.04
  +#		FROM nvidia/cuda:6.5-runtime-ubuntu14.04
   
   RUN apt-get update && apt-get install -y --no-install-recommends \
   		ubuntu-desktop \
  
positive.code: 		unzip bowtie2-2.3.3.1-linux-x86_64.zip && \
  		mv bowtie2-2.3.3.1-linux-x86_64/ bowtie2/ && \
  		rm bowtie2-2.3.3.1-linux-x86_64.zip
  ENV PATH $PATH:/bowtie2
  
  # Get NextGenMap source, build, and install into /usr/local/bin including openCL driver libs
  
  
negative.code: 
  # Copy nvBowtie and nvBWT executables to /usr/local/bin/
  
  COPY nvBowtie /usr/local/bin/
  COPY 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.2.8.2-1-ubuntu64.tar.gz && \
  		rm sratoolkit.2.8.2-1-ubuntu64.tar.gz
  ENV PATH ${PATH}:/sratoolkit.2.8.2-1-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 && \
  		cd /HaSAPPy/program && \
  		chmod +x PreprocessReads
  
  # Generate annotation databases
  RUN python /HaSAPPy/program/GeneReference_built.py -i /HaSAPPy/docs/mm10_REFSEQgenes.txt -o /HaSAPPy/docs/GeneReference_Mouse-MM10.pkl
  # --- !!--- RUN python /HaSAPPy/program/GeneReference_built.py -i  /HaSAPPy/docs/RefSeq_human_GRCh38-hg38.txt -o /HaSAPPy/docs/GeneReference_Homo.pkl
  
  
  # --------------- INIT -------------------------------
  