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Dockerfile
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# syntax=docker/dockerfile:1
# tu może rocker zamiast ubuntu
FROM ubuntu:18.04
RUN apt-get update -y && apt-get -y upgrade
RUN apt-get install -y build-essential wget gfortran xorg-dev libpcre3-dev \
libncurses5-dev zlib1g-dev libbz2-dev liblzma-dev libcurl3-dev git fort77 libreadline-dev bc libjpeg-dev curl default-jre nano
RUN apt-get install -y python3.6
RUN ln -s /usr/bin/python3.6 /usr/bin/python
WORKDIR /opt
RUN wget https://cran.r-project.org/src/base/R-3/R-3.4.3.tar.gz && \
tar xzf R-3.4.3.tar.gz && \
rm R-3.4.3.tar.gz && \
cd R-3.4.3/ && \
./configure && \
make && \
make install
RUN wget https://cran.r-project.org/src/contrib/Archive/MASS/MASS_7.3-50.tar.gz && \
R CMD INSTALL MASS_7.3-50.tar.gz && \
wget https://cran.r-project.org/src/contrib/Archive/VGAM/VGAM_1.0-5.tar.gz && \
R CMD INSTALL VGAM_1.0-5.tar.gz && \
wget https://cran.r-project.org/src/contrib/Archive/data.table/data.table_1.11.2.tar.gz && \
R CMD INSTALL data.table_1.11.2.tar.gz
RUN wget https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2 && \
tar xjf samtools-1.10.tar.bz2 && \
rm samtools-1.10.tar.bz2 && \
cd samtools-1.10 && \
./configure --prefix $(pwd) && \
make
ENV PATH=${PATH}:/opt/samtools-1.10
RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.27.1/bedtools-2.27.1.tar.gz && \
tar -zxvf bedtools-2.27.1.tar.gz && \
rm bedtools-2.27.1.tar.gz && \
cd bedtools2 && \
make
ENV PATH=${PATH}:/opt/bedtools2/bin
RUN git clone https://github.com/lh3/bwa.git && \
cd bwa && \
make
ENV PATH=${PATH}:/opt/bwa
RUN wget https://github.com/samtools/bcftools/releases/download/1.10.2/bcftools-1.10.2.tar.bz2 && \
tar -vxjf bcftools-1.10.2.tar.bz2 && \
cd bcftools-1.10.2 && \
./configure --prefix=/where/to/install && \
make && \
make install
ENV PATH=${PATH}/opt/bcftools-1.10.2/bin:$PATH
WORKDIR /opt
RUN apt-get install -y python3-pip
RUN apt-get clean && apt-get purge && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
RUN git clone https://github.com/HuMingLab/MAPS.git
WORKDIR /app
# todo fix package installation via pip3 and requirements
RUN pip3 install --upgrade pip
COPY requirements.txt requirements.txt
RUN pip3 install -r requirements.txt
RUN pip3 install -U setuptools
RUN pip3 install Cython~=0.29
RUN pip3 install cykhash macs3
RUN pip3 install deeptools
RUN pip3 install plumbum
RUN curl -s https://get.nextflow.io | bash && mv nextflow /opt/
RUN wget https://github.com/ijuric/MAPS/raw/refs/heads/master/bin/feather/juicer_tools.1.7.5_linux_x64_jcuda.0.8.jar && mv juicer_tools.1.7.5_linux_x64_jcuda.0.8.jar /opt/
RUN wget https://github.com/SFGLab/nf-hichip/archive/refs/tags/1.10.tar.gz && tar -xvzf 1.10.tar.gz && mv nf-hichip-1.10/* . && rm 1.10.tar.gz && rm -r nf-hichip-1.10
RUN /opt/nextflow
# || true is in case of some readonly files that are system-related
RUN chmod -R 777 / || true