Tool dockerization

.dockerignore

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+.git/
+docs/
+Dockerfile

.github/workflows/dockerhub.yml

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+name: dockerhub
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Remove leading v from the release tag
+        id: rmv
+        run: |
+          sansv=$(echo ${{ github.event.release.tag_name }} | tr -d v)
+          echo "::set-output name=tag::${{ github.repository }}:$sansv"
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      -
+        name: Login to DockerHub
+        uses: docker/login-action@v1 
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      -
+        name: Build and push
+        id: docker_build
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          tags: ${{steps.rmv.outputs.tag}}
+      -
+        name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}
+

.gitpod.yml

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+ports:
+  - port: 6080
+    onOpen: open-preview
+tasks:
+  - init: |
+      eval $(command gp env -e)
+      pip install synapseclient
+      synapse -u "$SYN_USER" -p "$SYN_TOKEN" \
+        get syn27202293 --downloadLocation /workspace/testdata
+      synapse -u "$SYN_USER" -p "$SYN_TOKEN" \
+        get syn27202298 --downloadLocation /workspace/testdata/csv
+      synapse -u "$SYN_USER" -p "$SYN_TOKEN" \
+        get syn28413455 --downloadLocation /workspace/testdata/mask
+      synapse -u "$SYN_USER" -p "$SYN_TOKEN" \
+        get syn27202398 --downloadLocation /workspace/testdata/seg
+      synapse -u "$SYN_USER" -p "$SYN_TOKEN" \
+        get syn27204544 --downloadLocation /workspace/testdata/tif
+      cp /workspace/cylinter/cylinter/config.yml /workspace/testdata

Dockerfile

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+FROM gitpod/workspace-full-vnc:latest
+
+# Qt5 graphics libraries for napari
+RUN sudo apt-get update && \
+    sudo apt-get install -y \
+        libpython3.8-dev \
+        qtbase5-dev \
+        qtchooser \
+        qt5-qmake \
+        qtbase5-dev-tools && \
+    sudo rm -rf /var/lib/apt/lists/*
+
+RUN python -m pip install "napari[all]"
+
+# Install cylinter
+COPY --chown=gitpod:gitpod . /app
+RUN python -m pip install /app
+
+RUN chmod +x /app/cylinter/start.sh
+CMD [ "/bin/bash", "-ci", "/app/cylinter/start.sh" ]

cylinter/config.yml

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 # GENERAL PROGRAM CONFIGURATIONS
 
-inDir: /Users/<username>/Desktop/cylinter_demo
+inDir: /data
 # Path to CyLinter input directory containing multi-channel
 # image files (TIFF or OME-TIFF), segmentation outlines (OME-TIFF),
 # segmentation masks (TIFF), and corresponding single-cell feature tables (CSV)
 
-outDir: /Users/<username>/Desktop/cylinter_demo/output
+outDir: /data/output
 # CyLinter output directory. Path is created if it does not exist.
 
 sampleMetadata:

cylinter/start.sh

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+#!/bin/bash
+
+/usr/bin/gp-vncsession
+cylinter /data/config.yml

setup.py

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 from setuptools import setup, find_packages
 
-with open("README.md", "r", encoding="utf-8") as fh:
+with open("ReadMe.md", "r", encoding="utf-8") as fh:
     LONG_DESCRIPTION = fh.read()
 
 requires = [