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Merge pull request #29 from rasools/OMICSINT_H24
Omicsint h24
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{ | ||
"recommendations": [ | ||
"bogem.bogems-night-owl" | ||
] | ||
} |
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docker build --platform=linux/amd64 -t docker.io/rasoolsnbis/omicsint_h24:unsupervisedOMICsIntegration-1.0.0 -f "session_ml/UnsupervisedOMICsIntegration/Dockerfile" "session_ml/UnsupervisedOMICsIntegration" | ||
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docker run -d -p 8787:8787 --platform=linux/amd64 --name my_rstudio_container docker.io/rasoolsnbis/omicsint_h24:unsupervisedOMICsIntegration-1.0.0 | ||
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FROM ubuntu:20.04 AS base | ||
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ARG RSTUDIO_ARCH="amd64" | ||
ARG RSTUDIO_VERSION="2023.12.1+402" | ||
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SHELL ["/bin/bash", "-o", "pipefail", "-c"] | ||
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# Set locale configs | ||
ENV LANG=en_US.UTF-8 | ||
ENV LANGUAGE=en_US.UTF-8 | ||
ENV LC_ALL=en_US.UTF-8 | ||
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# Install useful Linux packages and cleanup | ||
RUN export DEBIAN_FRONTEND=noninteractive \ | ||
&& apt-get -yq update \ | ||
&& apt-get -yq install --no-install-recommends \ | ||
curl \ | ||
dpkg-sig \ | ||
libpq5 \ | ||
psmisc \ | ||
sudo \ | ||
lsb-release \ | ||
libclang-dev \ | ||
locales \ | ||
ca-certificates \ | ||
libxml2 \ | ||
libodbc1 \ | ||
libglpk-dev \ | ||
&& echo "en_US.UTF-8 UTF-8" > /etc/locale.gen \ | ||
&& locale-gen \ | ||
&& rm -rf /var/lib/apt/lists/* | ||
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# Install Miniconda and Mamba | ||
RUN curl -LOs https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \ | ||
&& bash Miniconda3-latest-Linux-x86_64.sh -bfp /usr/local/miniconda3 \ | ||
&& rm Miniconda3-latest-Linux-x86_64.sh \ | ||
&& /usr/local/miniconda3/bin/conda install -n base -c conda-forge mamba \ | ||
&& ln -s /usr/local/miniconda3/bin/mamba /usr/local/bin/mamba | ||
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# Set up environment | ||
ENV PATH="/usr/local/miniconda3/bin:${PATH}" | ||
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# Install R | ||
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \ | ||
&& echo 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/' >> /etc/apt/sources.list \ | ||
&& apt-get -yq update \ | ||
&& apt-get -yq install --no-install-recommends \ | ||
r-base \ | ||
&& apt-get clean \ | ||
&& rm -rf /var/lib/apt/lists/* \ | ||
&& apt-get autoremove -yq && apt-get autoclean -yq | ||
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# Install necessary libraries for GLIBCXX_3.4.29 | ||
RUN apt-get -yq update \ | ||
&& apt-get -yq install --no-install-recommends \ | ||
software-properties-common \ | ||
&& add-apt-repository ppa:ubuntu-toolchain-r/test \ | ||
&& apt-get -yq update \ | ||
&& apt-get -yq install --no-install-recommends \ | ||
libstdc++6 \ | ||
&& apt-get clean \ | ||
&& rm -rf /var/lib/apt/lists/* | ||
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# INSTALL R packages using Mamba | ||
COPY UnsupervisedOMICsIntegration_env.yml /tmp/UnsupervisedOMICsIntegration_env.yml | ||
RUN mamba env create -f /tmp/UnsupervisedOMICsIntegration_env.yml \ | ||
&& rm /tmp/UnsupervisedOMICsIntegration_env.yml | ||
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# Download and install RStudio Server | ||
RUN curl -sL "https://download2.rstudio.org/server/focal/${RSTUDIO_ARCH}/rstudio-server-${RSTUDIO_VERSION//+/-}-${RSTUDIO_ARCH}.deb" -o /tmp/rstudio-server.deb && \ | ||
echo "64044984a5791690586e21bf4411019ed3dccaf32a69e0838090762f3eba8da0 /tmp/rstudio-server.deb" | sha256sum -c - && \ | ||
dpkg -i /tmp/rstudio-server.deb && \ | ||
rm -f /tmp/rstudio-server.deb && \ | ||
echo "lock-type=advisory" > /etc/rstudio/file-locks \ | ||
&& echo "www-frame-origin=same" >> /etc/rstudio/rserver.conf | ||
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# Common environment variables | ||
ENV USER=jovyan | ||
ENV GROUP=users | ||
ENV PASSWORD=default | ||
ENV DISABLE_AUTH=1 | ||
ENV UID=1000 | ||
ENV HOME=/home/${USER} | ||
ENV R_HOME=usr/lib/R | ||
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RUN useradd -s /bin/bash -N -u ${UID} -l ${USER} \ | ||
&& mkdir -p ${HOME} \ | ||
&& echo "${USER}:password123" | chpasswd \ | ||
&& chown -R ${USER}:${GROUP} ${HOME} \ | ||
&& chown -R ${USER}:${GROUP} /etc/rstudio/ \ | ||
&& chown -R ${USER}:${GROUP} /var/run/rstudio-server/ \ | ||
&& chown -R ${USER}:${GROUP} /usr/lib/rstudio-server/ \ | ||
&& chown -R ${USER}:${GROUP} /var/lib/rstudio-server/ | ||
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# R needs TZ set | ||
RUN echo "TZ=Etc/UTC" >> ${R_HOME}/etc/Renviron.site | ||
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# Set default CRAN repo to RSPM (it has pre-compiled R packages, increasing user install speed) | ||
RUN echo 'options(repos=c(CRAN="https://packagemanager.rstudio.com/all/__linux__/focal/latest"))' >> ${R_HOME}/etc/Rprofile.site \ | ||
&& echo 'options(HTTPUserAgent=sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os)))' >> ${R_HOME}/etc/Rprofile.site | ||
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WORKDIR ${HOME} | ||
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COPY run.sh /etc/run.sh | ||
RUN chmod +x /etc/run.sh | ||
COPY lab ${HOME}/lab | ||
RUN chmod +x ${HOME}/lab | ||
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USER ${USER} | ||
EXPOSE 8787 | ||
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ENTRYPOINT ["/etc/run.sh"] |
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session_ml/UnsupervisedOMICsIntegration/UnsupervisedOMICsIntegration_env.yml
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name: UnsupervisedOMICsIntegration | ||
channels: | ||
- defaults | ||
- conda-forge | ||
- bioconda | ||
dependencies: | ||
- r-ggplot2 | ||
- r-rmarkdown | ||
- r-knitr | ||
- r-plotly | ||
- r-dplyr | ||
- r-tidyr | ||
- r-mixomics | ||
- bioconductor-mofa2 | ||
- r-reticulate | ||
- mofapy2 | ||
- scipy==1.8.1 |
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