anchor.diff:  RUN git clone -b 'v1.0.4-beta' --single-branch --depth 1 https://github.com/vetscience/Tools
   RUN mv RepeatMasker-open-4-0-7.tar.gz /usr/local
   WORKDIR /usr/local
  +RUN wget http://www.repeatmasker.org/RepeatMasker-open-4-0-7.tar.gz
   RUN tar zxf RepeatMasker-open-4-0-7.tar.gz && rm -rf RepeatMasker-open-4-0-7.tar.gz
   WORKDIR RepeatMasker
  -RUN zcat /root/Dfam.hmm.gz > Libraries/Dfam.hmm && mv Libraries /root && ln -s /var/spool/cwl/Libraries .
  +RUN wget http://www.dfam.org/web_download/Release/Dfam_2.0/Dfam.hmm.gz
  +RUN zcat Dfam.hmm.gz > Libraries/Dfam.hmm && mv Libraries /root && ln -s /var/spool/cwl/Libraries .
  +RUN rm Dfam.hmm.gz
   RUN cp /root/Tools/Cwl/repeatmasker/RepeatMaskerConf/DateRepeats .
   RUN cp /root/Tools/Cwl/repeatmasker/RepeatMaskerConf/DupMasker .
   RUN cp /root/Tools/Cwl/repeatmasker/RepeatMaskerConf/ProcessRepeats .
  
positive.code: FROM ubuntu:16.04
  RUN apt-get update && apt-get install -y wget perl build-essential cpio less git
  WORKDIR /root
  RUN wget http://www.repeatmasker.org/RepeatModeler/RepeatModeler-open-1.0.11.tar.gz
  RUN wget http://www.repeatmasker.org/RepeatMasker-open-4-0-7.tar.gz
  RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz
  RUN wget http://www.repeatmasker.org/isb-2.6.0+-changes-vers2.patch.gz
  RUN wget http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz
  RUN wget http://www.repeatmasker.org/RepeatModeler/RECON-1.08.tar.gz
  RUN wget http://www.repeatmasker.org/RepeatScout-1.0.5.tar.gz
  RUN wget -r ftp://ftp.ncbi.nih.gov/pub/seg/nseg/
  RUN mv ftp.ncbi.nih.gov/pub/seg/nseg/ . && rm -rf ftp.ncbi.nih.gov/
  RUN wget http://www.dfam.org/web_download/Release/Dfam_2.0/Dfam.hmm.gz
  
  # Install NCBI rmblast
  RUN tar xvfz ncbi-blast-2.6.0+-src.tar.gz && gunzip isb-2.6.0+-changes-vers2.patch.gz
  WORKDIR ncbi-blast-2.6.0+-src
  RUN patch -p1 < /root/isb-2.6.0+-changes-vers2.patch
  WORKDIR c++
  RUN ./configure --with-mt --prefix=/usr/local/rmblast --without-debug
  RUN sed '54,55d' Makefile > Makefile.new && mv Makefile.new Makefile
  RUN make && make install
  
  # Install HMMER
  WORKDIR /root
  RUN tar zxf hmmer-3.1b2-linux-intel-x86_64.tar.gz
  WORKDIR hmmer-3.1b2-linux-intel-x86_64
  RUN ./configure && make && make install
  
  # Install RECON
  WORKDIR /root
  RUN tar zxf RECON-1.08.tar.gz
  WORKDIR RECON-1.08/src
  RUN make && make install
  WORKDIR /root/RECON-1.08/scripts
  
negative.code: RUN mv recon.pl.new recon.pl && chmod uog+x recon.pl
  
  # Install nseg
  WORKDIR /root
  RUN wget -r ftp://ftp.ncbi.nih.gov/pub/seg/nseg/
  WORKDIR /root/ftp.ncbi.nih.gov/pub/seg/nseg/
  RUN make && mv nseg /usr/local/bin && mv nmerge /usr/local/bin
  WORKDIR /root
  RUN rm -rf ftp.ncbi.nih.gov
  
  # Install RepeatScout
  RUN wget http://www.repeatmasker.org/RepeatScout-1.0.5.tar.gz
  RUN tar zxf RepeatScout-1.0.5.tar.gz
  WORKDIR RepeatScout-1
  RUN make && mv build_lmer_table /usr/local/bin && mv RepeatScout /usr/local/bin
  WORKDIR /root
  RUN rm -rf RepeatScout-1*
  
  # Install TRF
  RUN wget https://tandem.bu.edu/cgi-bin/trf/trf.download.pl?fileselect=30
  