anchor.diff:  ONBUILD ADD repeatmaskerlibraries.tar.gz /usr/local/RepeatMasker
   ONBUILD WORKDIR /usr/local/RepeatMasker
   ONBUILD RUN util/buildRMLibFromEMBL.pl Libraries/RepeatMaskerLib.embl > Libraries/RepeatMasker.lib && \
  -    makeblastdb -dbtype nucl -in Libraries/RepeatMasker.lib > /dev/null 2>&1 && \
  -    makeblastdb -dbtype nucl -in Libraries/RepeatPeps.lib > /dev/null 2>&1
  +        makeblastdb -dbtype nucl -in Libraries/RepeatMasker.lib > /dev/null 2>&1 && \
  +        makeblastdb -dbtype nucl -in Libraries/RepeatPeps.lib > /dev/null 2>&1
   ONBUILD RUN perl -i -0pe 's/^#\!.*perl.*/#\!\/usr\/bin\/perl/g' \
  -     RepeatMasker \
  -     DateRepeats \
  -     ProcessRepeats \
  -     RepeatProteinMask \
  -     DupMasker \
  -     util/queryRepeatDatabase.pl \
  -     util/queryTaxonomyDatabase.pl \
  -     util/rmOutToGFF3.pl \
  -     util/rmToUCSCTables.pl
  +        RepeatMasker \
  +        DateRepeats \
  +        ProcessRepeats \
  +        RepeatProteinMask \
  +        DupMasker \
  +        util/queryRepeatDatabase.pl \
  +        util/queryTaxonomyDatabase.pl \
  +        util/rmOutToGFF3.pl \
  +        util/rmToUCSCTables.pl
   ONBUILD RUN perl -0p -e 's/\/usr\/local\/hmmer/\/usr\/bin/g;' \
  -         -e 's/\/usr\/local\/rmblast/\/usr\/local\/bin/g;' \
  -         -e 's/DEFAULT_SEARCH_ENGINE = "crossmatch"/DEFAULT_SEARCH_ENGINE = "ncbi"/g;' \ 
  -         -e 's/TRF_PRGM = ""/TRF_PRGM = "\/usr\/local\/bin\/trf"/g;' RepeatMaskerConfig.tmpl > RepeatMaskerConfig.pm
  +        -e 's/\/usr\/local\/rmblast/\/usr\/local\/bin/g;' \
  +        -e 's/DEFAULT_SEARCH_ENGINE = "crossmatch"/DEFAULT_SEARCH_ENGINE = "ncbi"/g;' \ 
  +        -e 's/TRF_PRGM = ""/TRF_PRGM = "\/usr\/local\/bin\/trf"/g;' RepeatMaskerConfig.tmpl > RepeatMaskerConfig.pm
   
   ENV PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/RepeatMasker:/usr/local/RepeatScout
   #ENTRYPOINT ["/usr/local/RepeatMasker/RepeatMasker"]
  
positive.code: RUN apt-get update && apt-get install -qqy \
      wget \
      hmmer \
  	build-essential
  
  
  # Install TRF (for RepeatScout)
  WORKDIR /usr/local/bin
  
negative.code: 
  # Install nseg (for RepeatScout)
  RUN mkdir nseg && \
      cd nseg && \
      wget ftp://ftp.ncbi.nih.gov/pub/seg/nseg/* && \
      make && \
      mv nseg ../bin && \
      mv nmerge ../bin
  
  # Install RepeatScout
  RUN wget http://bix.ucsd.edu/repeatscout/RepeatScout-1.0.5.tar.gz && \
      tar -xvf RepeatScout* && \
      rm RepeatScout*.tar.gz && \
      mv RepeatScout* RepeatScout && \
      cd RepeatScout && \
      make	
  
  # Install RMBlast
  RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/2.2.28/ncbi-rmblastn-2.2.28-x64-linux.tar.gz && \
  