New container for stitching-spark

stitching-spark/1.10.0/Dockerfile

@@ -0,0 +1,44 @@
+ARG SPARK_VERSION=3.1.3
+ARG STITCHING_SPARK_GIT_TAG=1.10.0
+
+# Temporary container for building cleanly
+FROM janeliascicomp/builder:1.2.1 as builder
+ARG STITCHING_SPARK_GIT_TAG
+
+# Checkout and build the code
+WORKDIR /tmp/app
+# TODO: currently this points to a fork which adds a minor feature. It can be switched back to https://github.com/saalfeldlab/stitching-spark after the PR is merged.
+RUN git clone --branch ${STITCHING_SPARK_GIT_TAG} --depth 1 https://github.com/krokicki/stitching-spark.git . \
+    && git submodule update --init --recursive \
+    && /usr/local/bin/buildinfo.sh \
+    && mvn package
+
+# Find the built jar, based on the version in the pom file
+RUN xq -r '.project.artifactId+"-"+.project.version+".jar"' pom.xml > filename \
+    && mv /tmp/app/target/`cat filename` app.jar
+
+RUN echo "$STITCHING_SPARK_GIT_TAG" > /tmp/app/VERSION
+
+# Create final image
+FROM multifish/biocontainers-spark:${SPARK_VERSION}
+ARG STITCHING_SPARK_GIT_TAG
+
+MAINTAINER biocontainers <[email protected]>
+LABEL software="stitching-spark" \
+    base_image="apache/spark" \
+    container="stitching-spark" \
+    about.summary="Reconstructing large microscopy images from overlapping image tiles on a high-performance Spark cluster" \
+    about.home="https://github.com/saalfeldlab/stitching-spark" \
+    software.version=${STITCHING_SPARK_GIT_TAG} \
+    upstream.version=${STITCHING_SPARK_GIT_TAG} \
+    version="1" \
+    about.license="SPDX:GPL-2.0" \
+    about.license_file="/app/LICENSE.txt" \
+    extra.binaries="/opt/spark/bin" \
+    about.tags="implemented-in::java, interface::commandline, role::program"
+
+WORKDIR /app
+COPY --from=builder /tmp/app/LICENSE.txt /app/LICENSE
+COPY --from=builder /tmp/app/VERSION /app
+COPY --from=builder /tmp/app/app.jar /app
+COPY --from=builder /buildinfo /app