dockerfile_1

# Start with Ubuntu base image
FROM ubuntu:22.04

# Set environment variables to prevent prompts during package installation
ENV DEBIAN_FRONTEND=noninteractive

# Update and install dependencies
RUN apt-get update && apt-get install -y \
    software-properties-common \
    build-essential \
    curl \
    wget \
    zstd \
    gzip \
    libbz2-dev \
    libssl-dev \
    libffi-dev \
    zlib1g-dev \
    liblzma-dev \
    && rm -rf /var/lib/apt/lists/*

# Add deadsnakes PPA for Python 3.12
RUN add-apt-repository ppa:deadsnakes/ppa && \
    apt-get update && apt-get install -y \
    python3.12 \
    python3.12-dev \
    && rm -rf /var/lib/apt/lists/*

# Manually install pip for Python 3.12
RUN curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py && \
    python3.12 get-pip.py && \
    rm get-pip.py

# Add Python 3.12 to PATH and force link creation
RUN ln -sf /usr/bin/python3.12 /usr/local/bin/python && \
    ln -sf /usr/bin/python3.12 /usr/bin/python && \
    ln -sf /usr/bin/python3.12 /usr/bin/python3

# Install required Python packages
RUN python3.12 -m pip install pandas textdistance pyarrow

# Verify installation of Python and libraries
RUN python3.12 -m pip show pandas textdistance pyarrow

dockerfile_2

FROM mambaorg/micromamba:1.5.10 AS micromamba
# docker build -t chasemc2/text:0.0.1 .

COPY env.yaml /tmp/env.yaml

RUN micromamba install -y -n base -f /tmp/env.yaml && \
    micromamba clean --all --yes

USER $MAMBA_USER
ARG MAMBA_DOCKERFILE_ACTIVATE=1

env.yml

name: sgnf-hmmer

channels:
  - conda-forge
  - bioconda
  - defaults

dependencies:
  - conda-forge::python==3.12
  - conda-forge::gzip
  - pandas
  - textdistance
  - pyarrow
  - zstandard