Release

envs/Dockerfile

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+FROM nvidia/cuda:12.1.1-base-ubuntu22.04
+LABEL maintainer="Balázs Ligeti <obbalasz@gmail.com>"
+
+# Avoid prompts from apt
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install necessary packages
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    unzip \
+    lbzip2 \
+    mc \
+    libgtextutils-dev \
+    sudo \
+    curl \
+    gpg \
+    git \
+    && rm -rf /var/lib/apt/lists/*
+
+# Create and switch to the 'prokbert' user before installing Miniconda
+RUN useradd -m -s /bin/bash prokbert
+USER prokbert
+WORKDIR /home/prokbert
+
+# Install Miniconda as 'prokbert'
+RUN mkdir -p /home/prokbert/bin && \
+    cd /home/prokbert/bin && \
+    wget https://repo.anaconda.com/miniconda/Miniconda3-py311_23.10.0-1-Linux-x86_64.sh && \
+    chmod +x Miniconda3-py311_23.10.0-1-Linux-x86_64.sh && \
+    ./Miniconda3-py311_23.10.0-1-Linux-x86_64.sh -b -p /home/prokbert/miniconda3 && \
+    /home/prokbert/miniconda3/bin/conda init bash && \
+    echo "source /home/prokbert/miniconda3/etc/profile.d/conda.sh" >> /home/prokbert/.bashrc
+
+# Set PATH to include the user's conda and potentially other user-specific binaries
+ENV PATH /home/prokbert/miniconda3/bin:$PATH
+
+
+# Use pip to install prokbert and other dependencies
+RUN pip install prokbert seaborn umap-learn jupyterlab
+
+# Set up a work directory for prokbert stuff
+RUN git clone https://github.com/nbrg-ppcu/prokbert.git
+USER prokbert
+
+CMD ["/bin/bash"]

envs/prokbert.def

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+Bootstrap: docker
+From: nvidia/cuda:12.1.1-base-ubuntu22.04
+
+%labels
+    MAINTAINER Balázs Ligeti <obbalasz@gmail.com>
+
+%environment
+    DEBIAN_FRONTEND=noninteractive
+    PATH=/opt/miniconda3/bin:$PATH
+
+%post
+    # Install necessary packages
+    apt-get update && apt-get install -y --no-install-recommends \
+        wget \
+        unzip \
+        lbzip2 \
+        mc \
+        libgtextutils-dev \
+        sudo \
+        curl \
+        gpg \
+        git \
+        && rm -rf /var/lib/apt/lists/*
+
+    # Check if Miniconda is already installed; if not, install it
+    if [ ! -d "/opt/miniconda3" ]; then
+        echo "Installing Miniconda..."
+        wget https://repo.anaconda.com/miniconda/Miniconda3-py311_23.10.0-1-Linux-x86_64.sh -O /tmp/miniconda.sh
+        bash /tmp/miniconda.sh -b -p /opt/miniconda3
+        rm /tmp/miniconda.sh
+    else
+        echo "/opt/miniconda3 exists. Skipping Miniconda installation."
+    fi
+
+    echo "source /opt/miniconda3/etc/profile.d/conda.sh" >> $SINGULARITY_ENVIRONMENT
+
+    # Install Python packages
+    /opt/miniconda3/bin/pip install prokbert seaborn umap-learn jupyterlab
+
+    # Clone the prokbert repository
+    git clone https://github.com/nbrg-ppcu/prokbert.git /opt/prokbert
+
+%runscript
+    # Define what happens when the container is run without specifying a command
+    exec /opt/miniconda3/bin/python "$@"
+
+%help
+    This container includes the prokbert environment with Miniconda and additional Python packages.