added Dockerfile + custom init script

Dockerfile

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+# using ubuntu LTS version
+# from https://luis-sena.medium.com/creating-the-perfect-python-dockerfile-51bdec41f1c8
+
+# using ubuntu LTS version
+FROM ubuntu:20.04
+
+RUN apt-get update && apt-get install --no-install-recommends -y python3.8-dev \
+    python3.8-venv python3-pip python3-wheel build-essential && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# create and activate virtual environment
+RUN python3.8 -m venv /opt/venv
+ENV PATH="/opt/venv/bin:$PATH"
+
+# Install Poetry
+RUN python3 -m pip install pipx && \ 
+    python3 -m pipx ensurepath && \
+    pipx install poetry && \
+    pipx ensurepath
+
+# Set up environment variables for Poetry
+ENV PATH="$PATH:/root/.local/bin"
+ENV POETRY_HOME="/root/.poetry"
+
+# export path
+ENV PATH="$PATH:/root/.local/share/pipx/venvs/poetry/bin/"
+
+# Install Pandas and Keras in a virtual environment using Poetry
+WORKDIR /app
+
+# Copy only the pyproject.toml and poetry.lock files initially to leverage Docker cache
+COPY pyproject.toml ./
+
+# upgrade pip
+RUN pip install --upgrade pip setuptools wheel
+
+# Install dependencies
+#RUN poetry install --no-root -vvv
+
+# Copy the rest of the application code
+COPY . .
+
+# append Python module dir to Path
+RUN PATH="${PATH}:/app/modules"
+
+# Set the default command to run the application
+CMD ["python", "framepool_annotate.py"]

framepool_annotate.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Feb  8 07:26:34 2023
+
+Script to invoke FramePool annotation provided an input dataframe path
+
+@author: bbowles
+"""
+
+import sys
+sys.path.append('/app/modules/')
+from kipoi_functions import framepool_caller
+
+def main():
+    # Create an argument parser
+    parser = argparse.ArgumentParser(description="Annotate an ORFA file with FramePool ribosome load prediction.")
+
+    # Add the "--input" argument
+    parser.add_argument("--input", help="Input, tab-delimited ORFA file.", required=True)
+
+    # Parse the command line arguments
+    args = parser.parse_args()
+
+    # Get and print the full path
+    path = args.input
+
+    if path.endswith(".tsv"):
+
+        # run FramePool
+        scored_df = framepool_caller(path)
+
+        # save output
+        outpath = path.replace(".tsv",".framepool.tsv")
+        scored_df.to_csv(outpath, index=False, sep='\t')
+        print(f"Saved FramePool-annotated output to {outpath}.")
+
+    else:
+        raise Exception("Input file must end with .tsv!")
+
+if __name__ == "__main__":
+    main()