anchor.diff:  RUN wget -q https://github.com/biod/sambamba/releases/download/v0.6.7/sambamba_v0.6.7_linux.tar.bz2
   RUN tar xvjf sambamba_v0.6.7_linux.tar.bz2
   
  +#ENV PATH=$PATH:/augustus/bin:/augustus/scripts:/hal/bin:/WiggleTools/bin:/
  +#ENV LD_LIBRARY_PATH=/libBigWig:$LD_LIBRARY_PATH
  +
  +# Slimmer final Docker image
  +
  +FROM ubuntu:18.04
  +RUN apt-get update
  +RUN apt-get install -y wget bedtools bamtools samtools sqlite3 python-pip libgsl0-dev libcolamd2
  +# Kent
  +RUN for i in wigToBigWig faToTwoBit gff3ToGenePred genePredToBed genePredToFakePsl bamToPsl transMapPslToGenePred pslPosTarget axtChain chainMergeSort pslMap pslRecalcMatch pslMapPostChain gtfToGenePred genePredToGtf bedtools pslCheck pslCDnaFilter clusterGenes pslToBigPsl bedSort bedToBigBed ; do wget -q http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/$i -O /bin/$i ; chmod +x /bin/$i ; done
  +RUN wget -q http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat -O /bin/blat ; chmod +x /bin/blat
  +
  +COPY --from=builder /hal/bin/* /bin/
  +COPY --from=builder /sambamba /bin/
  +COPY --from=builder /augustus/bin/* /bin/
  +COPY --from=builder /augustus/scripts/* /bin/
  +COPY --from=builder /WiggleTools/bin/* /bin/
  +
  +RUN mkdir -p /augustus
  +COPY --from=builder /augustus/config /augustus/config
  +
   # Python deps
   RUN pip install bd2k-python-lib toil pyfasta numpy
   
  -ENV PATH=$PATH:/augustus/bin:/augustus/scripts:/hal/bin:/WiggleTools/bin:/
  -ENV AUGUSTUS_CONFIG_PATH=/augustus/config/
  -ENV LD_LIBRARY_PATH=/libBigWig:$LD_LIBRARY_PATH
  +ENV AUGUSTUS_CONFIG_PATH=/augustus/config/
positive.code: RUN cd augustus && git reset --hard ${AUGUSTUS_COMMIT}
  RUN echo 'COMPGENEPRED = true' >> augustus/common.mk
  RUN echo 'SQLITE = true' >> augustus/common.mk
  RUN cd augustus && make
  RUN cd augustus/src && make clean all
  RUN cd augustus/auxprogs/homGeneMapping/src && sed 's/# BOOST = true/BOOST = true/g' -i Makefile && sed 's/# SQLITE = true/SQLITE = true/g' -i Makefile
  RUN cd augustus/auxprogs && make clean && make
  
  # HDF5
  RUN wget -q http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1.tar.gz
  
negative.code: FROM ubuntu:18.04 AS builder
  ARG AUGUSTUS_COMMIT=e2dff65
  RUN apt-get update
  RUN apt-get install -y build-essential libssl-dev libncurses5-dev libcurl4-openssl-dev liblzma-dev libbz2-dev libboost-all-dev sqlite3 libsqlite3-0 libsqlite3-dev libgsl0-dev lp-solve liblpsolve55-dev libbamtools-dev wget git
  
  # htslib
  RUN git clone git://github.com/samtools/htslib.git
  