From 4f0cfebf854d26a1c84b91ba4521f9d30eff3dfa Mon Sep 17 00:00:00 2001
From: Daniel Cameron <d-cameron@github.com>
Date: Thu, 23 Dec 2021 14:54:15 +1100
Subject: [PATCH] #548 Initial attempt at docker CI

---
 .github/workflows/docker.yml  | 40 +++++++++++++++++++++++++++++++++++
 Dockerfile                    | 12 +++++------
 scripts/dev/create_release.sh |  3 ---
 3 files changed, 46 insertions(+), 9 deletions(-)
 create mode 100644 .github/workflows/docker.yml

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
new file mode 100644
index 00000000..4d049feb
--- /dev/null
+++ b/.github/workflows/docker.yml
@@ -0,0 +1,40 @@
+name: docker-ci
+
+on:
+  push:
+    branches:
+      - master
+      - dev
+  pull_request:
+    branches:
+      - master
+      - dev
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Checkout
+        uses: actions/checkout@v2
+        with:
+          submodules: 'recursive'
+      -
+        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: ${{ secrets.DOCKERHUB_TOKEN }}
+      -
+        name: Build and push
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          push: false
+          tags: gridss/gridss:latest
\ No newline at end of file
diff --git a/Dockerfile b/Dockerfile
index 6b307dc6..928fd509 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,8 +1,9 @@
 ARG UBUNTU_VERSION=20.04
-# Use the closest mirror so apt-get doesnt take ages
 FROM ubuntu:$UBUNTU_VERSION AS gridss_base_closest_mirror
+# Use the closest mirror so apt-get doesnt take ages
 RUN sed -i -e 's/http:\/\/archive\.ubuntu\.com\/ubuntu\//mirror:\/\/mirrors\.ubuntu\.com\/mirrors\.txt/' /etc/apt/sources.list
-# compile GRIDSS C code
+
+# Set up a C build environment for gridsstools, samtools, and R packages
 FROM gridss_base_closest_mirror AS gridss_c_build_environment
 RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
 	libssl-dev \
@@ -12,7 +13,6 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
 	libbz2-dev \
 	liblzma-dev \
 	libdeflate-dev \
-	libncurses5-dev \
 	build-essential \
 	autotools-dev \
 	autoconf \
@@ -22,10 +22,10 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
 	libomp-dev \
 	&& rm -rf /var/lib/apt/lists/*
 
+# compile gridsstools
 FROM gridss_c_build_environment AS gridss_builder_c
 RUN mkdir /opt/gridss/
 ARG GRIDSS_VERSION
-# compile gridsstools
 COPY src/main/c /opt/gridss/src/main/c
 COPY src/test/resources /opt/gridss/src/test/resources
 RUN cd /opt/gridss/src/main/c/gridsstools/htslib && \
@@ -33,6 +33,7 @@ RUN cd /opt/gridss/src/main/c/gridsstools/htslib && \
 	cd .. && \
 	autoreconf -i && ./configure && make -j 8 && \
 	cp gridsstools /opt/gridss/
+
 # compile GRIDSS Java code
 FROM maven:3.6.3-jdk-8 AS gridss_builder_java
 RUN mkdir /opt/gridss/
@@ -40,8 +41,7 @@ WORKDIR /opt/gridss/
 # Download maven dependencies first so docker can cache them
 COPY pom.xml /opt/gridss/
 COPY repo /opt/gridss/repo
-#RUN mvn -Dmaven.artifact.threads=8 dependency:go-offline
-# run all stages so all dependencies are 
+# run all stages so all dependencies are cached
 RUN mvn -Dmaven.artifact.threads=8 verify && rm -rf target
 # Build GRIDSS jar
 ARG GRIDSS_VERSION
diff --git a/scripts/dev/create_release.sh b/scripts/dev/create_release.sh
index 6623d71b..f1db8f25 100644
--- a/scripts/dev/create_release.sh
+++ b/scripts/dev/create_release.sh
@@ -28,7 +28,6 @@ mv src/main/c/gridsstools-src-$version.tar.gz release/
 cp LICENSE release/ # https://bioconda.github.io/contributor/linting.html#gpl-requires-license-distributed
 docker build --build-arg GRIDSS_VERSION=$version --target gridss_export_build_artefacts --output type=local,dest=release . # --progress=plain
 docker build --build-arg GRIDSS_VERSION=$version --target gridss -t gridss/gridss:$version -t gridss/gridss:latest .
-docker build --build-arg GRIDSS_VERSION=$version --target gridss_minimal -t gridss/gridss_minimal:$version -t gridss/gridss_minimal:latest .
 docker build --build-arg GRIDSS_VERSION=$version --target gridss -t gridss/virusbreakend:$version -t gridss/virusbreakend:latest .
 cd release
 chmod +x *
@@ -36,8 +35,6 @@ chmod -x *.R *.jar
 tar czf gridss-$version.tar.gz *
 echo docker push gridss/gridss:$version 
 echo docker push gridss/gridss:latest
-echo docker push gridss/gridss_minimal:$version
-echo docker push gridss/gridss_minimal:latest 
 echo docker push gridss/virusbreakend:$version
 echo docker push gridss/virusbreakend:latest