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Dockerfile
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FROM ubuntu:20.04
MAINTAINER [email protected]
ENV SRC /usr/local/src
ENV BIN /usr/local/bin
RUN apt-get update && apt-get install -y software-properties-common && \
apt-get update && apt-get install --no-install-recommends -y \
build-essential \
python3 \
python3-pip \
python-setuptools \
python3-distutils \
python3.8-venv \
bzip2 \
tini \
libboost-all-dev \
libcurl3-dev \
libbz2-dev \
liblzma-dev \
libncurses5-dev \
unzip \
wget \
zlib1g \
zlib1g-dev \
libdeflate-dev \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
apt-get clean && \
apt-get autoremove -y && \
rm -rf /var/lib/{apt,dpkg,cache,log}/
RUN ln -sf /usr/bin/python3 /usr/bin/python
RUN pip install numpy==1.24.4 build twist pysam==0.21.0 matplotlib==3.5.2 biopython==1.81
ENV SAMTOOLS_VERSION=1.9
RUN SAMTOOLS_URL="https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2" && \
cd $SRC && \
wget $SAMTOOLS_URL && \
tar xvf samtools-${SAMTOOLS_VERSION}.tar.bz2 && \
cd samtools-${SAMTOOLS_VERSION}/htslib-${SAMTOOLS_VERSION} && ./configure && make && make install && \
cd ../ && ./configure --without-curses && make && make install && cd $SRC && rm -r samtools-${SAMTOOLS_VERSION}/htslib-${SAMTOOLS_VERSION}
ENV BOWTIE_VERSION=2.5.4
WORKDIR $SRC
RUN wget https://github.com/BenLangmead/bowtie2/releases/download/v${BOWTIE_VERSION}/bowtie2-${BOWTIE_VERSION}-linux-x86_64.zip -O bowtie2-${BOWTIE_VERSION}-linux-x86_64.zip && \
unzip bowtie2-${BOWTIE_VERSION}-linux-x86_64.zip && \
mv bowtie2-${BOWTIE_VERSION}-linux-x86_64/bowtie2* $BIN && \
rm *.zip && \
rm -r bowtie2-${BOWTIE_VERSION}-linux-x86_64
ENV STAR_VERSION=2.7.8a
RUN STAR_URL="https://github.com/alexdobin/STAR/archive/${STAR_VERSION}.tar.gz" &&\
wget -P $SRC $STAR_URL &&\
tar -xvf $SRC/${STAR_VERSION}.tar.gz -C $SRC && \
mv $SRC/STAR-${STAR_VERSION}/bin/Linux_x86_64_static/STAR /usr/local/bin && rm -r $SRC/STAR-${STAR_VERSION}
RUN mkdir -p easyquant
COPY . easyquant
RUN cd easyquant && python -m build && pip install dist/*.whl
WORKDIR /
ENTRYPOINT ["tini", "--"]
CMD [ "/bin/bash" ]