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FROM ubuntu
ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
RUN apt-get update --fix-missing && \
apt-get install -y wget bzip2 ca-certificates curl git && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
RUN echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
wget --quiet https://repo.continuum.io/miniconda/Miniconda3-4.4.10-Linux-x86_64.sh -O ~/miniconda.sh && \
/bin/bash ~/miniconda.sh -b -p /opt/conda && \
rm ~/miniconda.sh && \
/opt/conda/bin/conda clean -tipsy
ENV TINI_VERSION v0.16.1
ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /usr/bin/tini
RUN chmod +x /usr/bin/tini
ENV PATH $PATH:/opt/conda/bin
ENTRYPOINT [ "/usr/bin/tini", "--" ]
CMD [ "/bin/bash" ]
COPY environment.yml /
RUN conda env create -f /environment.yml
ENV PATH /opt/conda/envs/tf-activity/bin:$PATH
# Install container-wide requrements gcc, pip, zlib, libssl, make, libncurses, fortran77, g++, R
RUN apt-get update && \
apt-get install -y \
git \
gcc \
g++ \
make \
perl \
wget \
build-essential \
libbz2-dev \
libcurl4-openssl-dev \
liblzma-dev \
libncurses5-dev \
libpcre3-dev \
libreadline-dev \
libssl-dev \
curl \
zip \
unzip \
zlib1g-dev
# Install HOMER
RUN mkdir /opt/homer
RUN curl -fsSL http://homer.ucsd.edu/homer/configureHomer.pl -o /opt/homer/configureHomer.pl
RUN perl /opt/homer/configureHomer.pl -install
# Install MEME
RUN curl -fsSL meme-suite.org/meme-software/4.12.0/meme_4.12.0.tar.gz -o /opt/meme_4.12.0.tar.gz
RUN cd /opt/ && tar -xzf /opt/meme_4.12.0.tar.gz
RUN cd /opt/meme_4.12.0; ./configure --prefix=/opt/meme --enable-build-libxml2 --enable-build-libxslt; \
make; make install
COPY assets/JASPAR2018_CORE_vertebrates_nr_pfms.homer /
COPY assets/JASPAR2018_CORE_vertebrates_nr_pfms.jaspar /
COPY assets/merged_concat_tfs/* /merged_concat_tfs_encode/
ENV PATH $PATH:/opt/homer/bin:/opt/meme/bin