diff Docker/Dockerfile @ 0:c051e9688932 draft default tip

planemo upload for repository https://github.com/goeckslab/gleam.git commit 11356473f09dd54d86af28b74bd9ed097d07ca04

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Docker/Dockerfile	Thu Jul 03 23:48:01 2025 +0000
@@ -0,0 +1,58 @@
+FROM debian:stable
+
+LABEL maintainer="Paulo Lyra" \
+      version="1.0.0" \
+      description="Docker image for PyHIST Galaxy tool"
+
+# Install necessary tools
+RUN export DEBIAN_FRONTEND=noninteractive && \
+    apt-get update --fix-missing -qq && \
+    apt-get install -y -q \
+    build-essential \
+    libgl1-mesa-glx \
+    python3 \
+    python3-pip \
+    python3-venv \
+    openslide-tools \
+    python3-openslide \
+    libmagic-dev \
+    git && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Set working directory
+WORKDIR /pyhist
+
+# Clone PyHIST repository
+RUN git clone https://github.com/manuel-munoz-aguirre/PyHIST.git . && \
+    git checkout master
+
+# Create and activate virtual environment, then install Python packages
+RUN python3 -m venv /pyhist/venv && \
+    /pyhist/venv/bin/pip install --upgrade pip && \
+    /pyhist/venv/bin/pip install \
+    pandas \
+    opencv-python \
+    numpy \
+    Pillow \
+    python-magic \
+    openslide-python \
+    psutil
+
+# Compile segmentation algorithm
+RUN cd src/graph_segmentation/ && \
+    make && \
+    chmod 755 segment
+
+# Add venv binaries to PATH
+ENV PATH="/pyhist/venv/bin:$PATH"
+
+# Make pyhist.py globally executable and accessible
+RUN chmod +x /pyhist/pyhist.py && \
+    ln -s /pyhist/pyhist.py /usr/local/bin/pyhist
+
+# Ensure src directory is in PYTHONPATH for module imports
+ENV PYTHONPATH="/pyhist:$PYTHONPATH"
+
+# Set default command (optional, for debugging)
+CMD ["/bin/bash"]