add all changes from the previous PR

.github/workflows/pr.yml

@@ -0,0 +1,30 @@
+name: PR
+
+on:
+  pull_request:
+    branches: [ "main", "master" ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  initialise:
+    runs-on: ubuntu-latest
+
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+  build_only:
+    needs: initialise
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Build docker image
+        uses: docker/build-push-action@v6
+        with:
+          push: false
+          tags: user/app:latest

.github/workflows/release.yml

@@ -0,0 +1,34 @@
+name: release-CI
+
+on:
+  release:
+    types: [published]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  build_and_publish:
+    runs-on: ubuntu-latest
+
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Login to Quay IO
+        uses: docker/login-action@v3
+        with:
+          registry: quay.io
+          username: '$oauthtoken'
+          password: ${{ secrets.QUAY_OAUTH_TOKEN }}
+
+      - name: Build docker image and push to quay.io
+        uses: docker/build-push-action@v6
+        with:
+          push: true
+          tags: |
+            quay.io/bgruening/webatlas:${{ github.event.release.tag_name }}
+            quay.io/bgruening/webatlas:latest

.gitignore

@@ -0,0 +1,171 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# PyPI configuration file
+.pypirc

Dockerfile

@@ -0,0 +1,48 @@
+FROM python:3.10-slim-bookworm AS builder
+
+ARG BIOFORMATS2RAW="0.7.0"
+ARG WEBATLAS_FORK_TAG="0.5.3-galaxy4"
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+      wget unzip cmake g++ && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Download and stage bioformats2raw
+RUN wget -q -O bioformats2raw.zip https://github.com/glencoesoftware/bioformats2raw/releases/download/v${BIOFORMATS2RAW}/bioformats2raw-${BIOFORMATS2RAW}.zip && \
+    unzip bioformats2raw.zip -d /opt/ && \
+    rm bioformats2raw.zip
+
+# Download and stage webatlas scripts
+RUN wget -q -O webatlas.tar.gz https://github.com/dannyspadaro/webatlas-pipeline/archive/refs/tags/${WEBATLAS_FORK_TAG}.tar.gz && \
+    tar -xf webatlas.tar.gz && \
+    mkdir /opt/webatlas-bin && \
+    cp -r webatlas-pipeline-${WEBATLAS_FORK_TAG}/bin/* /opt/webatlas-bin/ && \
+    chmod +x /opt/webatlas-bin/* && \
+    rm -rf webatlas.tar.gz webatlas-pipeline-${WEBATLAS_FORK_TAG}
+
+COPY requirements.txt /requirements.txt
+RUN pip install --upgrade pip "setuptools<81" distlib --no-cache-dir && \
+    pip install --no-cache-dir -r /requirements.txt
+
+# Runtime stage
+FROM python:3.10-slim-bookworm
+
+ARG BIOFORMATS2RAW="0.7.0"
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+      libblosc1 libvips libtiff-tools openjdk-17-jre-headless procps && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Copy required from builder
+COPY --from=builder /opt/bioformats2raw-${BIOFORMATS2RAW} /usr/local/share/bioformats2raw-${BIOFORMATS2RAW}
+RUN ln -sf /usr/local/share/bioformats2raw-${BIOFORMATS2RAW}/bin/bioformats2raw /usr/local/bin/bioformats2raw
+
+COPY --from=builder /opt/webatlas-bin/ /usr/local/bin/
+COPY --from=builder /usr/local/lib/python3.10 /usr/local/lib/python3.10
+COPY --from=builder /usr/local/bin /usr/local/bin
+
+ENTRYPOINT []

README.md

@@ -1,2 +1,4 @@
 # docker-webatlas
 Docker image for Galaxy WebAtlas toolsuite
+
+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

@@ -0,0 +1,18 @@
+pillow==12.0.0
+xmlschema==4.3.1
+scipy==1.15.3
+fire==0.7.1
+regex==2026.2.28
+scikit-image==0.25.2
+tifffile==2025.5.10
+numpy==2.2.6
+pandas==2.3.3
+pyvips==3.1.1
+scanpy==1.11.5
+ome-zarr==0.10.2
+anndata==0.11.4
+zarr==2.16.1
+h5py==3.16.0
+rioxarray==0.19.0
+spatialdata==0.5.0
+vitessce==3.8.2