fix: add Docker workflow and update mpralib version to 0.10.5

.github/workflows/docker.yml

@@ -0,0 +1,67 @@
+---
+name: Build and Push Docker Image
+
+on: # yamllint disable-line rule:truthy
+  push:
+    branches: [master, development]
+    paths:
+      - .github/workflows/docker.yml
+      - version.mpralib.txt
+      - workflow/envs/Dockerfile_mpralib
+  workflow_dispatch:
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6
+
+      - name: Read mpralib version from version file
+        id: mpralib_version
+        run: |
+          VERSION=$(tr -d '[:space:]' < version.mpralib.txt)
+          if [[ -z "$VERSION" ]]; then
+            echo "version.mpralib.txt is empty"
+            exit 1
+          fi
+          if [[ ! "$VERSION" =~ ^[0-9]+(\.[0-9]+)*$ ]]; then
+            echo "Invalid version format in version.mpralib.txt: $VERSION"
+            exit 1
+          fi
+          echo "version=$VERSION" >> "$GITHUB_OUTPUT"
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v4
+        with:
+          username: ${{ vars.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Check if Docker tag already exists
+        id: tag_exists
+        run: |
+          TAG="visze/mpralib:${{ steps.mpralib_version.outputs.version }}"
+          if docker manifest inspect "$TAG" > /dev/null 2>&1; then
+            echo "exists=true" >> "$GITHUB_OUTPUT"
+            echo "Tag already exists on Docker Hub: $TAG"
+          else
+            echo "exists=false" >> "$GITHUB_OUTPUT"
+            echo "Tag does not exist yet: $TAG"
+          fi
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v4
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v4
+
+      - name: Build and push Docker image
+        if: steps.tag_exists.outputs.exists == 'false'
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: workflow/envs/Dockerfile_mpralib
+          push: true
+          tags: visze/mpralib:${{ steps.mpralib_version.outputs.version }}
+          build-args: |
+            MPRALIB_VERSION=${{ steps.mpralib_version.outputs.version }}

version.mpralib.txt

@@ -0,0 +1 @@
+0.10.5

workflow/envs/Dockerfile_mpralib

@@ -1,3 +1,5 @@
 FROM ghcr.io/prefix-dev/pixi:latest
 
-RUN pixi global install "python>=3.10" "mpralib==0.10.4" "htslib"  conda -c conda-forge -c bioconda
+ARG MPRALIB_VERSION
+
+RUN pixi global install "python>=3.10" "mpralib==${MPRALIB_VERSION}" "htslib" conda -c conda-forge -c bioconda

workflow/envs/mpralib.yaml

@@ -4,5 +4,5 @@ channels:
   - bioconda
 dependencies:
   - python>=3.10
-  - mpralib==0.10.4
+  - mpralib==0.10.5
   - htslib

workflow/rules/common.smk

@@ -4,6 +4,7 @@ from snakemake.utils import validate
 
 SCRIPTS_DIR = "../scripts"
 ENVS_DIR = "../envs"
+MPRALIB_VERSION_FILE = "../../version.mpralib.txt"
 
 
 def getWorkflowFile(dir_name, name):
@@ -18,6 +19,19 @@ def getCondaEnv(name):
     return getWorkflowFile(ENVS_DIR, name)
 
 
+def getMpralibVersion():
+    with open(workflow.source_path(MPRALIB_VERSION_FILE)) as f:
+        mpralib_version = f.read().strip()
+    if not mpralib_version:
+        raise WorkflowError("version.mpralib.txt is empty.")
+    return mpralib_version
+
+
+MPRALIB_VERSION = getMpralibVersion()
+VISZE_MPRALIB_CONTAINER = f"docker://visze/mpralib:{MPRALIB_VERSION}"
+QUAY_MPRALIB_CONTAINER = f"docker://quay.io/biocontainers/mpralib:{MPRALIB_VERSION}--pyhdfd78af_0"
+
+
 def getLabelFile():
     if "label_file" in config:
         return config["label_file"]

workflow/rules/elements.smk

@@ -11,7 +11,7 @@ rule get_element_counts:
     conda:
         getCondaEnv("mpralib.yaml")
     container:
-        "docker://quay.io/biocontainers/mpralib:0.10.4--pyhdfd78af_0"
+        QUAY_MPRALIB_CONTAINER
     threads: 1
     resources:
         mem_mb=lambda wc, input: calc_mem_gb(input[0], 75) * 1024,  # Adjust memory based on input size
@@ -85,7 +85,7 @@ rule get_reporter_elements:
     conda:
         getCondaEnv("mpralib.yaml")
     container:
-        "docker://quay.io/biocontainers/mpralib:0.10.4--pyhdfd78af_0"
+        QUAY_MPRALIB_CONTAINER
     threads: 1
     resources:
         mem_mb=lambda wc, input: calc_mem_gb(input[0], 50) * 1024,  # Adjust memory based on input size
@@ -116,7 +116,7 @@ rule get_reporter_genomic_elements:
     conda:
         getCondaEnv("mpralib.yaml")
     container:
-        "docker://visze/mpralib:0.10.4"
+        VISZE_MPRALIB_CONTAINER
     threads: 1
     resources:
         mem_mb=lambda wc, input: calc_mem_gb(input[0], 50) * 1024,  # Adjust memory based on input size

workflow/rules/variants.smk

@@ -11,7 +11,7 @@ rule get_variant_counts:
     conda:
         getCondaEnv("mpralib.yaml")
     container:
-        "docker://quay.io/biocontainers/mpralib:0.10.4--pyhdfd78af_0"
+        QUAY_MPRALIB_CONTAINER
     threads: 1
     resources:
         mem_mb=lambda wc, input: calc_mem_gb(input[0], 75) * 1024,  # Adjust memory based on input size
@@ -44,7 +44,7 @@ rule get_variant_map:
     conda:
         getCondaEnv("mpralib.yaml")
     container:
-        "docker://quay.io/biocontainers/mpralib:0.10.4--pyhdfd78af_0"
+        QUAY_MPRALIB_CONTAINER
     threads: 1
     resources:
         mem_mb=lambda wc, input: calc_mem_gb(input[0], 10) * 1024,  # Adjust memory based on input size
@@ -135,7 +135,7 @@ rule get_reporter_variants:
     conda:
         getCondaEnv("mpralib.yaml")
     container:
-        "docker://quay.io/biocontainers/mpralib:0.10.4--pyhdfd78af_0"
+        QUAY_MPRALIB_CONTAINER
     threads: 1
     resources:
         mem_mb=lambda wc, input: calc_mem_gb(input[1], 75) * 1024,  # Adjust memory based on input size
@@ -168,7 +168,7 @@ rule get_reporter_genomic_variants:
     conda:
         getCondaEnv("mpralib.yaml")
     container:
-        "docker://visze/mpralib:0.10.4"
+        VISZE_MPRALIB_CONTAINER
     threads: 1
     resources:
         mem_mb=lambda wc, input: calc_mem_gb(input[1], 75) * 1024,  # Adjust memory based on input size