adds docker image and workflow

.github/workflows/docker-image.yml

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+name: build and push CI
+
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      - 'v*.*'
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Checkout
+        uses: actions/checkout@v4
+      -
+        name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          # list of Docker images to use as base name for tags
+          images: |
+            geertvangeest/cancer-variants-vscode
+          # generate Docker tags based on the following events/attributes
+          tags: |
+            type=semver,pattern={{major}}.{{minor}}
+
+      # -
+      #   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@v5
+        with:
+          push: true
+          context: ./Docker
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+

Docker/Dockerfile

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+FROM linuxserver/code-server:4.95.3
+
+# Install base utilities
+RUN apt-get update && \
+    apt-get install -y wget bc tree && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install mamba
+RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
+RUN bash Miniforge3-$(uname)-$(uname -m).sh -b -p /opt/miniforge3
+RUN /opt/miniforge3/condabin/mamba init
+
+# Put conda in path so we can use conda activate
+ENV PATH=/opt/miniforge3/condabin/:$PATH
+
+
+# intall required software with conda
+COPY environment.yml ./
+
+RUN mamba env create \
+    -n ngs-tools \
+    -f environment.yml
+
+RUN mamba init 
+
+COPY settings.json /config/data/User/
+COPY keybindings.json /config/data/User/
+RUN mkdir -p /config/project

Docker/environment.yml

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+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python>=3.8
+  - samtools>=1.12
+  - bwa=0.7.17
+  - snpeff>=5.0
+  - gatk4=4.5
+  - r-base
+  - cnvkit

Docker/keybindings.json

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+// Place your key bindings in this file to override the defaultsauto[]
+[
+    {
+        "key": "ctrl+enter",
+        "command": "workbench.action.terminal.runSelectedText"
+    }
+]

Docker/settings.json

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+{
+    "workbench.startupEditor": "none",
+    "extensions.ignoreRecommendations": true,
+    "extensions.showRecommendationsOnlyOnDemand": true,
+    "terminal.integrated.fontSize": 14,
+    "editor.fontSize": 13
+}