Merge pull request #28 from medema-group/feature/docker

Feature/docker

.github/workflows/docker.yml

@@ -0,0 +1,42 @@
+name: Create and publish a Docker image
+
+on:
+  push:
+    branches: 
+    - master
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v2
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.gitignore

@@ -0,0 +1,12 @@
+# ide stuff
+.vscode/
+
+# python stuff
+*.pyc
+
+# documentation build
+site/
+
+# test coverage report and svg
+.coverage
+coverage.svg

Dockerfile

@@ -9,13 +9,13 @@ WORKDIR /usr/src
 RUN git clone https://github.com/medema-group/BiG-SCAPE.git
 
 # Create conda environment
-RUN conda env create -f /usr/src/BiG-SCAPE/environment.yml
+RUN conda env create -f /usr/src/BiG-SCAPE/bigscape_dependencies.yml
 RUN echo "source activate bigscape" > ~/.bashrc
 ENV PATH /usr/local/envs/bigscape/bin:$PATH
 ENV PATH /usr/src/BiG-SCAPE:$PATH
 
 RUN cd BiG-SCAPE \
- && wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam34.0/Pfam-A.hmm.gz \
+ && wget https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz \
  && gunzip Pfam-A.hmm.gz \
  && source activate bigscape \
  && hmmpress Pfam-A.hmm \

run_bigscape

@@ -1,11 +1,12 @@
 #!/bin/bash
 
 if [[ $# -eq 0 || $1 == "-h" || $1 == "--help" || $1 == "--version" ]]; then
+	docker pull ghcr.io/medema-group/big-scape
 	docker run \
 	--detach=false \
 	--rm \
 	--user=$(id -u):$(id -g) \
-	docker-registry.wur.nl/medema-group/big-scape:1.1.2 \
+	ghcr.io/medema-group/big-scape \
 	$@
 else
 	set -o errexit
@@ -45,13 +46,14 @@ else
 	#if [ ${INPUT_FILE} ${OUTPUT_FILE} ]; then
 	if [ ! -z ${INPUT_FILE} ] && [ ! -z ${OUTPUT_FILE} ]; then
 		echo Running BiG-SCAPE
+		docker pull ghcr.io/medema-group/big-scape
 		docker run \
 	    	--volume ${INPUT_DIR}:${CONTAINER_SRC_DIR}:ro \
 	    	--volume ${OUTPUT_DIR}:${CONTAINER_DST_DIR}:rw \
 	    	--detach=false \
 	    	--rm \
 	    	--user=$(id -u):$(id -g) \
-	    	docker-registry.wur.nl/medema-group/big-scape:1.1.2 \
+	    	ghcr.io/medema-group/big-scape \
 	    	-i ${CONTAINER_SRC_DIR}/${INPUT_FILE} \
 	    	-o ${CONTAINER_DST_DIR}/${OUTPUT_FILE}\
     		$@