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Merge pull request #865 from Kincekara/update-phytreeviz
update phytreeviz
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| FROM python:3.9.17-slim as app | ||
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| # 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" | ||
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| # '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="${PHYTREEVIZ_VER}" | ||
| LABEL description="Visualizing phylogenetic trees" | ||
| LABEL website="https://github.com/moshi4/phyTreeViz/" | ||
| LABEL license="https://github.com/moshi4/phyTreeViz/blob/main/LICENSE" | ||
| LABEL maintainer="Erin Young" | ||
| LABEL maintainer.email="[email protected]" | ||
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| # 'RUN' executes code during the build | ||
| # Install dependencies via apt-get or yum if using a centos or fedora base | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| procps \ | ||
| ca-certificates && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| # Install and/or setup more things. Make /data for use as a working dir | ||
| # For readability, limit one install per 'RUN' statement. | ||
| RUN pip install --no-cache phytreeviz==${PHYTREEVIZ_VER} | ||
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| ENV PATH="$PATH" \ | ||
| LC_ALL=C | ||
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| # 'CMD' instructions set a default command when the container is run. This is typically 'tool --help.' | ||
| CMD phytreeviz --help | ||
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| # 'WORKDIR' sets working directory | ||
| WORKDIR /data | ||
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| ##### ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ##### | ||
| ##### 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. ##### | ||
| ##### ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ##### | ||
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| # A second FROM insruction creates a new stage | ||
| FROM app as test | ||
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| RUN apt-get update && apt-get install -y --no-install-recommends wget unzip | ||
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| # set working directory so that all test inputs & outputs are kept in /test | ||
| WORKDIR /test | ||
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| # 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 | ||
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| # Demonstrate that the program is successfully installed - which is highly dependant on what the tool is. | ||
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| # 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 |
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| # phyTreeViz container | ||
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| Main tool: [phyTreeViz](https://github.com/moshi4/phyTreeViz) | ||
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| Code repository: https://github.com/moshi4/phyTreeViz | ||
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| Basic information on how to use this tool: | ||
| - executable: phytreeviz | ||
| - help: --help | ||
| - version: --version | ||
| - description: Visualizing phylogenetic trees | ||
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| Additional information: | ||
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| > phyTreeViz is a simple and minimal phylogenetic tree visualization python package implemented based on matplotlib. This package was developed to enhance phylogenetic tree visualization functionality of BioPython. | ||
| This is contains a python library as well as a command line executable. | ||
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| Full documentation: | ||
| - CLI Docs : https://moshi4.github.io/phyTreeViz/cli-docs/phytreeviz/ | ||
| - API Docs : https://moshi4.github.io/phyTreeViz/api-docs/treeviz/ | ||
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| ## Example Usage | ||
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| CLI example | ||
| ```bash | ||
| phytreeviz -i input.nwk -o output.png | ||
| ``` | ||
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| API example | ||
| ```python | ||
| from phytreeviz import TreeViz, load_example_tree_file | ||
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| tree_file = load_example_tree_file("small_example.nwk") | ||
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| tv = TreeViz(tree_file) | ||
| tv.show_branch_length(color="red") | ||
| tv.show_confidence(color="blue") | ||
| tv.show_scale_bar() | ||
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| tv.savefig("api_example01.png", dpi=300) | ||
| ``` |