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Dockerfile
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FROM ubuntu:16.04
RUN apt-get update && apt-get install -y \
python2.7 \
make \
libc6-dev \
g++ \
zlib1g-dev \
build-essential \
git \
libx11-dev \
xutils-dev \
zlib1g-dev \
python-pip \
bowtie2 \
curl \
libncurses5-dev \
unzip \
wget
RUN pip install -U pip
RUN curl -O -L https://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2 && tar xvfj samtools-0.1.18.tar.bz2 && cd samtools-0.1.18 && make && cp samtools /usr/local/bin && cp bcftools/bcftools /usr/local/bin && cd misc/ && cp *.pl maq2sam-long maq2sam-short md5fa md5sum-lite wgsim /usr/local/bin/ && cd
RUN pip install scipy
RUN pip install biopython
RUN pip install git+https://github.com/katholt/srst2
# CD-HIT
RUN git clone https://github.com/weizhongli/cdhit.git && \
cd cdhit &&\
make MAX_SEQ=10000000 && \
cd