add dependencies for calling optional perl scripts

ENV PATH cellranger_convert:$PATH

RUN ln -s /cellranger_convert/convert.sh /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/bin/conversion

ENV LC_ALL C.UTF-8

ENV LANG C.UTF-8

RUN apt-get install -y \

 python3-pip \

 && python3 -m pip install --upgrade pip setuptools wheel \

 && pip3 install multiqc

RUN git clone https://github.com/linsalrob/fastq-pair.git \

 && cd fastq-pair \

 && mkdir build \

 && cd build \

 && gcc -std=gnu99   ../main.c ../robstr.c ../fastq_pair.c ../is_gzipped.c  -o fastq_pair \

 && cp fastq_pair /bin/fastq_pair