Merge pull request #29 from rasools/OMICSINT_H24

Omicsint h24

.vscode/extensions.json

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+{
+    "recommendations": [
+        "bogem.bogems-night-owl"
+    ]
+}

notes.sh

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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"
+
+docker run -d -p 8787:8787 --platform=linux/amd64 --name my_rstudio_container docker.io/rasoolsnbis/omicsint_h24:unsupervisedOMICsIntegration-1.0.0
+

session_ml/UnsupervisedOMICsIntegration/Dockerfile

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+FROM ubuntu:20.04 AS base
+
+ARG RSTUDIO_ARCH="amd64"
+ARG RSTUDIO_VERSION="2023.12.1+402"
+
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+
+# Set locale configs
+ENV LANG=en_US.UTF-8
+ENV LANGUAGE=en_US.UTF-8
+ENV LC_ALL=en_US.UTF-8
+
+# 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/*
+
+# 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
+
+# Set up environment
+ENV PATH="/usr/local/miniconda3/bin:${PATH}"
+
+# Install R
+RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \
+    && echo 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/' >> /etc/apt/sources.list \
+    && apt-get -yq update \
+    && apt-get -yq install --no-install-recommends \
+    r-base \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \ 
+    && apt-get autoremove -yq && apt-get autoclean -yq
+
+# Install necessary libraries for GLIBCXX_3.4.29
+RUN apt-get -yq update \
+    && apt-get -yq install --no-install-recommends \
+    software-properties-common \
+    && add-apt-repository ppa:ubuntu-toolchain-r/test \
+    && apt-get -yq update \
+    && apt-get -yq install --no-install-recommends \
+    libstdc++6 \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# INSTALL R packages using Mamba
+COPY UnsupervisedOMICsIntegration_env.yml /tmp/UnsupervisedOMICsIntegration_env.yml
+RUN mamba env create -f /tmp/UnsupervisedOMICsIntegration_env.yml \
+    && rm /tmp/UnsupervisedOMICsIntegration_env.yml
+
+# Download and install RStudio Server
+RUN curl -sL "https://download2.rstudio.org/server/focal/${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
+
+# 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
+
+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/
+
+# R needs TZ set
+RUN echo "TZ=Etc/UTC" >> ${R_HOME}/etc/Renviron.site
+
+# 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
+
+WORKDIR ${HOME}
+
+COPY run.sh /etc/run.sh
+RUN chmod +x /etc/run.sh
+COPY lab ${HOME}/lab
+RUN chmod +x ${HOME}/lab
+
+USER ${USER}
+EXPOSE 8787
+
+ENTRYPOINT ["/etc/run.sh"]

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