jysgro/samstat repository overview

⁠Samstat

Samstat from https://github.com/timolassmann/samstat⁠ compiled into Ubuntu

See that site for samstat usage modes.

⁠Container use

Run with either docker or podman

Simple run will simply write version:

• docker run -it --rm jysgro/samstat:2.2.3
• For podman: podman run -it --rm docker.io/jysgro/samstat:2.2.3

To bypass the default [CMD] command simply add another command or use with entrypoint:

• `docker run -it --rm --entrypoint /bin/bash -v ${PWD}:/data -w /data jysgro/samstat:2.2.3
• podman run -it --rm --entrypoint /bin/bash -v ${PWD}:/data -w /data docker.io/jysgro/samstat:2.2.3

Note that sharing current directory with ${PWD} is "universal" for Mac/Linux but also Windows, unlike $(pwd) that only works on Mac/Linux. The current directory is mapped to /data and thanks to -w the container will start with /data as the working directory. Note that /data can be any name you choose.

⁠Dockerfile

Created with the help of MS Copilot. I typically add also nano and wget utilities. [CMD] last line shows version by default, but can be overcome by adding another command or by using entrypoint. (See above)

# Start from an official Ubuntu base image
# FROM ubuntu:latest
FROM ubuntu:24.04

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

# Install system dependencies
RUN apt-get update && apt-get install -y \
    build-essential \
    cmake \
    git \
    libhdf5-dev \
    autoconf \
    automake \
    libtool \
    nano \
    wget \
    && rm -rf /var/lib/apt/lists/*

# Clone and build SAMstat
RUN git clone https://github.com/TimoLassmann/samstat.git /opt/samstat && \
    mkdir /opt/samstat/build && \
    cd /opt/samstat/build && \
    cmake .. && \
    make && \
    make install && \
    # Clean up build artifacts
    cd / && rm -rf /opt/samstat

# Set default command to show SAMstat version
CMD ["samstat", "--version"]