anchor.diff:  ## bowtie
   WORKDIR $SRC
   RUN wget https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.2.1.1/bowtie-1.2.1.1-linux-x86_64.zip/download -O bowtie-1.2.1.1-linux-x86_64.zip && \
  -        unzip bowtie-1.2.1.1-linux-x86_64.zip && \
  +    unzip bowtie-1.2.1.1-linux-x86_64.zip && \
   	mv bowtie-1.2.1.1/bowtie* $BIN
   
   
   ## RSEM
   RUN mkdir /usr/local/lib/site_perl
   WORKDIR $SRC
  -RUN wget https://github.com/deweylab/RSEM/archive/v1.3.0.tar.gz && \
  -    tar xvf v1.3.0.tar.gz && \
  -    cd RSEM-1.3.0 && \
  +RUN wget https://github.com/deweylab/RSEM/archive/v1.3.3.tar.gz && \
  +    tar xvf v1.3.3.tar.gz && \
  +    cd RSEM-1.3.3 && \
       make && \
  -    cp rsem-* $BIN && \
  +    cp rsem-* convert-sam-for-rsem $BIN && \
       cp rsem_perl_utils.pm /usr/local/lib/site_perl/ && \
  -    cd ../ && rm -r RSEM-1.3.0
  +    cd ../ && rm -r RSEM-1.3.3
   
   
   ## Kallisto
   WORKDIR $SRC
  -RUN wget https://github.com/pachterlab/kallisto/releases/download/v0.43.1/kallisto_linux-v0.43.1.tar.gz && \
  -    tar xvf kallisto_linux-v0.43.1.tar.gz && \
  -    mv kallisto_linux-v0.43.1/kallisto $BIN
  +RUN wget https://github.com/pachterlab/kallisto/releases/download/v0.46.1/kallisto_linux-v0.46.1.tar.gz && \
  +    tar xvf kallisto_linux-v0.46.1.tar.gz && \
  +    mv kallisto/kallisto $BIN
   
   
   ## FASTQC
  
positive.code: ENV GATK_HOME $SRC/gatk-${GATK_VERSION}
  
  
  
  ##########
  ## Trinity
  
  WORKDIR $SRC
  
  ENV TRINITY_VERSION="2.12.0-predevC"
  ENV TRINITY_CO="d47476d83cffa419af2abc9bcaaedf411e8c83f6"
  
  
negative.code:     chmod 755 /usr/local/src/FastQC/fastqc && \
      ln -s /usr/local/src/FastQC/fastqc $BIN/.
  
  # blast
  WORKDIR $SRC
  RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.5.0/ncbi-blast-2.5.0+-x64-linux.tar.gz && \
      tar xvf ncbi-blast-2.5.0+-x64-linux.tar.gz && \
      cp ncbi-blast-2.5.0+/bin/* $BIN && \
      rm -r ncbi-blast-2.5.0+
  
  ## Bowtie2
  WORKDIR $SRC
  