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FROM ubuntu:18.04
LABEL description="methyl-data analysis pipeline"
RUN apt-get update && apt-get install -y \
git \
g++ \
build-essential \
openjdk-8-jdk \
openjdk-8-jre \
perl \
wget \
curl \
cpanminus \
zlib1g \
zlib1g-dev \
python-pip \
python3-pip \
python \
vim \
tar
RUN apt-get update -y && \
apt-get upgrade -y && \
apt-get dist-upgrade -y && \
apt-get install build-essential software-properties-common -y && \
apt-get install libcurl4-openssl-dev -y && \
apt-get install libssl-dev -y && \
apt-get install libbz2-dev -y && \
apt-get update -y
RUN cpanm \
Math::Gauss \
Math::Round \
Bio::Trace::ABIF \
Spreadsheet::Write \
Statistics::Basic \
Parallel::ForkManager \
Sort::Key
ENV CONDA_DIR /opt/conda
ENV PATH $CONDA_DIR/bin:$PATH
RUN wget -q --no-check-certificate https://repo.anaconda.com/archive/Anaconda3-2022.05-Linux-x86_64.sh
RUN echo "a7c0afe862f6ea19a596801fc138bde0463abcbce1b753e8d5c474b506a2db2d *Anaconda3-2022.05-Linux-x86_64.sh" | sha256sum -c - && \
/bin/bash /Anaconda3-2022.05-Linux-x86_64.sh -f -b -p $CONDA_DIR && \
rm Anaconda3-2022.05-Linux-x86_64.sh && \
echo export PATH=$CONDA_DIR/bin:'$PATH' > /etc/profile.d/conda.sh
ENV TZ=Europe/Moscow
RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
RUN apt remove r-base
RUN add-apt-repository -r 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'
RUN apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
RUN add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/'
## R 4.1.3
RUN apt-get update -y
RUN apt-get install gdebi-core -y
RUN export R_VERSION=4.1.3
RUN curl -O https://cdn.rstudio.com/r/ubuntu-1804/pkgs/r-4.1.3_1_amd64.deb
RUN gdebi -nq /r-4.1.3_1_amd64.deb
RUN ln -s /opt/R/4.1.3/bin/R /usr/local/bin/R
RUN ln -s /opt/R/4.1.3/bin/Rscript /usr/local/bin/Rscript
RUN apt-get install -y pigz
RUN apt-get install libtbb2
RUN conda install -c bioconda bedtools
RUN conda install -c bioconda ucsc-fasize
RUN conda install -c bioconda ucsc-wigtobigwig
RUN conda install -c bioconda fastqc
RUN conda install -c bioconda samtools
## bs2
RUN pip2 install --upgrade setuptools
RUN pip2 install pysam
RUN conda install -c bioconda bowtie
## bismark
#RUN conda install -c bioconda bowtie2
RUN git clone https://github.com/BenLangmead/bowtie2.git
WORKDIR bowtie2
RUN make
WORKDIR /
ENV PATH /bowtie2:$PATH
#RUN conda install -c bioconda bismark
#RUN conda install -c bioconda/label/cf201901 bismark
RUN pip install multiqc
RUN pip install cutadapt
## trimgalore
RUN curl -fsSL https://github.com/FelixKrueger/TrimGalore/archive/0.6.6.tar.gz -o trim_galore.tar.gz
RUN tar xvzf trim_galore.tar.gz
ENV PATH /TrimGalore-0.6.6:$PATH
RUN mkdir -p /msPIPE
COPY lib /msPIPE/lib
COPY bin /msPIPE/bin
COPY msPIPE.py /msPIPE/
RUN wget -q https://github.com/bedops/bedops/releases/download/v2.4.39/bedops_linux_x86_64-v2.4.39.tar.bz2
RUN tar jxvf bedops_linux_x86_64-v2.4.39.tar.bz2
ENV PATH /msPIPE:$PATH
ENV PATH $CONDA_DIR/bin/cutadapt:$PATH
RUN Rscript /msPIPE/bin/script/Package_install.R
RUN mkdir -p /work_dir
WORKDIR /work_dir