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Merge pull request #2 from usegalaxy-eu/initial
add all changes from the previous PR
2 parents 619ec11 + d12d93c commit 49daf61

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‎.github/workflows/pr.yml‎

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name: PR
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on:
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pull_request:
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branches: [ "main", "master" ]
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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jobs:
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initialise:
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runs-on: ubuntu-latest
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steps:
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# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
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- uses: actions/checkout@v4
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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build_only:
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needs: initialise
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runs-on: ubuntu-latest
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steps:
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- name: Build docker image
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uses: docker/build-push-action@v6
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with:
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push: false
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tags: user/app:latest

‎.github/workflows/release.yml‎

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name: release-CI
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on:
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release:
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types: [published]
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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jobs:
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build_and_publish:
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runs-on: ubuntu-latest
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steps:
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# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
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- uses: actions/checkout@v4
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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- name: Login to Quay IO
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uses: docker/login-action@v3
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with:
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registry: quay.io
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username: '$oauthtoken'
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password: ${{ secrets.QUAY_OAUTH_TOKEN }}
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- name: Build docker image and push to quay.io
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uses: docker/build-push-action@v6
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with:
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push: true
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tags: |
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quay.io/bgruening/webatlas:${{ github.event.release.tag_name }}
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quay.io/bgruening/webatlas:latest

‎.gitignore‎

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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cover/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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.pybuilder/
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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# .python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# UV
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# Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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#uv.lock
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# poetry
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# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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#poetry.lock
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# pdm
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# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
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#pdm.lock
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# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
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# in version control.
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# https://pdm.fming.dev/latest/usage/project/#working-with-version-control
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.pdm.toml
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.pdm-python
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.pdm-build/
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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# PyCharm
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# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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#.idea/
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# PyPI configuration file
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.pypirc

‎Dockerfile‎

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FROM python:3.10-slim-bookworm AS builder
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ARG BIOFORMATS2RAW="0.7.0"
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ARG WEBATLAS_FORK_TAG="0.5.3-galaxy4"
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RUN apt-get update && \
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apt-get install -y --no-install-recommends \
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wget unzip cmake g++ && \
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apt-get clean && \
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rm -rf /var/lib/apt/lists/*
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# Download and stage bioformats2raw
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RUN wget -q -O bioformats2raw.zip https://github.com/glencoesoftware/bioformats2raw/releases/download/v${BIOFORMATS2RAW}/bioformats2raw-${BIOFORMATS2RAW}.zip && \
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unzip bioformats2raw.zip -d /opt/ && \
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rm bioformats2raw.zip
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# Download and stage webatlas scripts
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RUN wget -q -O webatlas.tar.gz https://github.com/dannyspadaro/webatlas-pipeline/archive/refs/tags/${WEBATLAS_FORK_TAG}.tar.gz && \
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tar -xf webatlas.tar.gz && \
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mkdir /opt/webatlas-bin && \
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cp -r webatlas-pipeline-${WEBATLAS_FORK_TAG}/bin/* /opt/webatlas-bin/ && \
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chmod +x /opt/webatlas-bin/* && \
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rm -rf webatlas.tar.gz webatlas-pipeline-${WEBATLAS_FORK_TAG}
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COPY requirements.txt /requirements.txt
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RUN pip install --upgrade pip "setuptools<81" distlib --no-cache-dir && \
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pip install --no-cache-dir -r /requirements.txt
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# Runtime stage
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FROM python:3.10-slim-bookworm
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ARG BIOFORMATS2RAW="0.7.0"
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RUN apt-get update && \
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apt-get install -y --no-install-recommends \
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libblosc1 libvips libtiff-tools openjdk-17-jre-headless procps && \
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apt-get clean && \
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rm -rf /var/lib/apt/lists/*
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# Copy required from builder
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COPY --from=builder /opt/bioformats2raw-${BIOFORMATS2RAW} /usr/local/share/bioformats2raw-${BIOFORMATS2RAW}
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RUN ln -sf /usr/local/share/bioformats2raw-${BIOFORMATS2RAW}/bin/bioformats2raw /usr/local/bin/bioformats2raw
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COPY --from=builder /opt/webatlas-bin/ /usr/local/bin/
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COPY --from=builder /usr/local/lib/python3.10 /usr/local/lib/python3.10
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COPY --from=builder /usr/local/bin /usr/local/bin
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ENTRYPOINT []

‎README.md‎

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# docker-webatlas
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Docker image for Galaxy WebAtlas toolsuite
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There are some minor changes that are required for Galaxy included in @dannyspadaro's fork: https://github.com/haniffalab/webatlas-pipeline/compare/main...dannyspadaro:webatlas-pipeline:update_dependencies

‎requirements.txt‎

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pillow==12.0.0
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xmlschema==4.3.1
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scipy==1.15.3
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fire==0.7.1
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regex==2026.2.28
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scikit-image==0.25.2
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tifffile==2025.5.10
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numpy==2.2.6
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pandas==2.3.3
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pyvips==3.1.1
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scanpy==1.11.5
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ome-zarr==0.10.2
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anndata==0.11.4
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zarr==2.16.1
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h5py==3.16.0
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rioxarray==0.19.0
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spatialdata==0.5.0
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vitessce==3.8.2

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