Install python package in docker file

Question

In my docker file, I want to install med2image python package (https://github.com/FNNDSC/med2image). I use the following code:

FROM ubuntu:16.04 RUN apt-get update && apt-get install -y --no-install-recommends \     python3.5 \     python3-pip \     && \ apt-get clean && \ rm -rf /var/lib/apt/lists/* RUN pip install nibabel pydicom matplotlib pillow RUN pip install med2image 

But I get the following error when I want to build the image:

Downloading https://files.pythonhosted.org/packages/6f/e5/948b023c7feb72adf7dfb26d90a13c838737bbf52be704f5ddd0878e3264/med2image-1.1.2.tar.gz Complete output from command python setup.py egg_info: Sorry, only Python 3.5+ is supported.  ---------------------------------------- Command "python setup.py egg_info" failed with error code 1 in  /tmp/pip-install-FnNb_S/med2image/ The command '/bin/sh -c pip install med2image' returned a non-zero code: 1 

What should I do?!

Answer 1

Recommended base image

As suggested in my comment, you could write a Dockerfile that looks like:

FROM python:3  RUN pip install --no-cache-dir --upgrade pip && \     pip install --no-cache-dir nibabel pydicom matplotlib pillow && \     pip install --no-cache-dir med2image  CMD ["cat", "/etc/os-release"] 

And the command example above could confirm at runtime (docker build --pull -t test . && docker run --rm -it test) that this image is based on the GNU/Linux distribution "Debian stable".

Generic Dockerfile template

Finally to give a comprehensive answer, note that a good practice regarding Python dependencies consists in specifying them in a declarative way in a dedicated text file (in alphabetical order, to ease review and update) so that for your example, you may want to write the following file:

requirements.txt

matplotlib med2image nibabel pillow pydicom 

and use the following generic Dockerfile

FROM python:3  WORKDIR /usr/src/app  COPY requirements.txt ./  RUN pip install --no-cache-dir --upgrade pip && \     pip install --no-cache-dir -r requirements.txt  COPY . .  CMD [ "python", "./your-daemon-or-script.py" ] 

To be more precise, this is the approach suggested in the documentation of the Docker official image python, §. How to use this image

Answer 2

Some of the other answers/comments are suggesting to change your base image but if you want to keep your ubuntu 16.04 you can also simply specify your version of pip/python to use pip3 or pip3.5 like shown below.

FROM ubuntu:16.04  RUN apt-get update && apt-get install -y --no-install-recommends \     python3.5 \     python3-pip \     && \     apt-get clean && \     rm -rf /var/lib/apt/lists/*  RUN pip3 install nibabel pydicom matplotlib pillow RUN pip3 install med2image