Dockerfile

FROM python:3.9.17-slim as app

# List all software versions are ARGs near the top of the dockerfile
# 'ARG' sets environment variables during the build stage
# ARG variables are ONLY available during image build, they do not persist in the final image
ARG PHYTREEVIZ_VER="0.2.0"

# 'LABEL' instructions tag the image with metadata that might be important to the user
LABEL base.image="python:3.9.17-slim"
LABEL dockerfile.version="1"
LABEL software="phyTreeViz"
LABEL software.version="${PHYTREEVIZ_VER}"
LABEL description="Visualizing phylogenetic trees"
LABEL website="https://github.com/moshi4/phyTreeViz/"
LABEL license="https://github.com/moshi4/phyTreeViz/blob/main/LICENSE"
LABEL maintainer="Erin Young"
LABEL maintainer.email="eriny@utah.gov"

# 'RUN' executes code during the build
# Install dependencies via apt-get or yum if using a centos or fedora base
RUN apt-get update && apt-get install -y --no-install-recommends \
    procps \
    ca-certificates && \
    apt-get autoclean && rm -rf /var/lib/apt/lists/*

# Install and/or setup more things. Make /data for use as a working dir
# For readability, limit one install per 'RUN' statement.
RUN pip install --no-cache phytreeviz==${PHYTREEVIZ_VER}

ENV PATH="$PATH" \
    LC_ALL=C

# 'CMD' instructions set a default command when the container is run. This is typically 'tool --help.'
CMD phytreeviz --help 

# 'WORKDIR' sets working directory
WORKDIR /data

##### ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- #####
##### Step 2. Set up the testing stage.                                 #####
##### The docker image is built to the 'test' stage before merging, but #####
##### the test stage (or any stage after 'app') will be lost.           #####
##### ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- #####

# A second FROM insruction creates a new stage
FROM app as test

RUN apt-get update && apt-get install -y --no-install-recommends wget unzip

# set working directory so that all test inputs & outputs are kept in /test
WORKDIR /test

# print help and version info; check dependencies (not all software has these options available)
# Mostly this ensures the tool of choice is in path and is executable
RUN phytreeviz --help && \
    phytreeviz --version

# Demonstrate that the program is successfully installed - which is highly dependant on what the tool is.

# Run the program's internal tests if available, for example with SPAdes:
RUN wget -q https://github.com/moshi4/phyTreeViz/raw/main/example/example.zip && \
    unzip example.zip && \
    phytreeviz -i ./example/small_example.nwk -o cli_example_small.png --show_branch_length --show_confidence && \
    phytreeviz -i ./example/medium_example.nwk -o cli_example_med.png --fig_height 0.3 --align_leaf_label && \
    ls cli_example_med.png cli_example_small.png