Initial commit: FlowDock pipeline configured for WES execution

Dockerfile

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+FROM pytorch/pytorch:2.2.1-cuda11.8-cudnn8-runtime
+
+LABEL authors="BioinfoMachineLearning"
+
+# Install system requirements
+RUN apt-get update && \
+    apt-get install -y --reinstall ca-certificates && \
+    apt-get install -y --no-install-recommends \
+        git \
+        wget \
+        libxml2 \
+        libgl-dev \
+        libgl1 \
+        gcc \
+        g++ \
+        procps && \
+    rm -rf /var/lib/apt/lists/*
+
+# Set working directory
+RUN mkdir -p /software/flowdock
+WORKDIR /software/flowdock
+
+# Clone FlowDock repository
+RUN git clone https://github.com/BioinfoMachineLearning/FlowDock /software/flowdock
+
+# Create conda environment
+RUN conda env create -f /software/flowdock/environments/flowdock_environment.yaml
+
+# Install local package and ProDy
+RUN /bin/bash -c "source /opt/conda/etc/profile.d/conda.sh && \
+    conda activate FlowDock && \
+    pip install --no-cache-dir -e /software/flowdock && \
+    pip install --no-cache-dir --no-dependencies prody==2.4.1"
+
+# Create checkpoints directory
+RUN mkdir -p /software/flowdock/checkpoints
+
+# Download pretrained weights
+RUN wget -q https://zenodo.org/records/15066450/files/flowdock_checkpoints.tar.gz && \
+    tar -xzf flowdock_checkpoints.tar.gz && \
+    rm flowdock_checkpoints.tar.gz
+
+# Activate conda environment by default
+RUN echo "source /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
+    echo "conda activate FlowDock" >> ~/.bashrc
+
+# Default shell
+SHELL ["/bin/bash", "-l", "-c"]
+CMD ["/bin/bash"]