anchor.diff:  	&& make \
   	&& make install \
   	&& make clean \
  -	&& cd /root ; rm -rf /root/vsearch-2* 
  +	&& cd /root ; rm -rf vsearch-2* v2*.tar.gz
  +
  +### install skewer
  +RUN cd /root \
  +    && git clone https://github.com/relipmoc/skewer \
  +    && cd skewer \
  +    && make \
  +    && make install \
  +    && make clean \
  +    && cd /root ; rm -rf skewer
  +
  +### install autoskewer
  +RUN cd /root \
  +    git clone http://github.com/MG-RAST/autoskewer \
  +    && cd autoskewer \
  +    && make
  +ENV PATH /root/autoskewer/:$PATH
   
   ### install CWL runner
   RUN pip install cwlref-runner
  
positive.code: 	&& cd blatSrc \
  	&& make BINDIR=/usr/local/bin/ \
  	&& strip /usr/local/bin/blat \
  	&& cd .. \
  	&& rm -rf blatSrc blatSrc35.zip
  
  ### install FragGeneScan from our patched source in github
  RUN cd /root \
  
negative.code: 	&& install -m755 -s fastq-multx /usr/local/bin \
  	&& install -m755 -s fastq-join /usr/local/bin \
  	&& install -m755 -s fastq-mcf /usr/local/bin \
  	&& cd /root ; rm -rf ea-utils
  
  ### install sortmerna
  RUN cd /root \
  	&& wget https://github.com/biocore/sortmerna/archive/2.1b.tar.gz \
  	&& tar xvf 2*.tar.gz \
  	&& cd sortmerna-2* \
  	&& sed -i 's/^\#define READLEN [0-9]*/#define READLEN 500000/' include/common.hpp \
  	&& ./configure \
      && make install \
      && make clean \
      && cd /root ; rm -rf sortmerna-2* 2*.tar.gz
  
  ### install vsearch 2.43
  RUN cd /root \
  