.github/workflows/release.yml

@@ -0,0 +1,32 @@
+name: Publish Docker image
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  push_to_registry:
+    name: Push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v4
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          images: geargenomics/dicey
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
+        with:
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.gitignore

@@ -1,6 +1,7 @@
 .sdsl
 .htslib
 bin/
+data/
 src/dicey
 src/sdslLite/
 *~

Dockerfile

@@ -1,5 +1,5 @@
 # use the ubuntu base image
-FROM ubuntu:18.04
+FROM ubuntu:22.04
 
 MAINTAINER Tobias Rausch rausch@embl.de
 
@@ -19,9 +19,11 @@ RUN apt-get update && apt-get install -y \
     libboost-filesystem-dev \
     libboost-iostreams-dev \
     libbz2-dev \
+    libdeflate-dev \
     libhdf5-dev \
     libncurses-dev \
     liblzma-dev \
+    pkg-config \
     zlib1g-dev \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/*
@@ -38,15 +40,16 @@ RUN cd /opt \
 
 # Multi-stage build
 FROM alpine:latest
+RUN apk add --no-cache bash
 RUN mkdir -p /opt/dicey/bin
 WORKDIR /opt/dicey/bin
 COPY --from=0 /opt/dicey/bin/dicey .
 
 # Workdir
-WORKDIR /root/
+WORKDIR /home
 
 # Add dicey to PATH
 ENV PATH="/opt/dicey/bin:${PATH}"
 
 # by default /bin/sh is executed
-CMD ["/bin/sh"]
+CMD ["/bin/bash"]