Adding quinine container (resolves #149)

quinine/Makefile

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+# Definitions
+build_path = build
+runtime_path = runtime
+build_output = ${runtime_path}/adam
+runtime_fullpath = $(realpath ${runtime_path})
+build_tool = runtime-container.DONE
+build_number ?= none
+git_commit ?= $(shell git rev-parse HEAD)
+name = quay.io/ucsc_cgl/quinine
+tag = 3e5f19bf1399e1447a42a2359c01be54d75b183d--${git_commit}
+
+# Steps
+build: ${build_output} ${build_tool}
+
+${build_output}: ${build_path}/Dockerfile
+ cd ${build_path} && docker build -t ${name}-build:${tag} . 
+ echo ${runtime_fullpath}
+ docker run -v ${runtime_fullpath}:/data ${name}-build:${tag} cp -r /home/quinine /data/quinine
+
+${build_tool}: ${build_output} ${runtime_path}/Dockerfile 
+ cd ${runtime_path} && docker build -t ${name}:${tag} .
+ touch ${build_tool}
+
+test: build
+ python test.py
+
+clean:
+ rm -rf runtime/quinine ${build_tool}
+ docker rmi -f ${name}-build:${tag} ${name}:${tag}
+
+push: build
+ # Requires ~/.dockercfg 
+ docker push ${name}:${tag}
+ docker push ${name}:latest

quinine/README.md

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+This directory contains the docker images for
+[Quinine](https://github.com/bigdatagenomics/quinine), which is a genomics
+quality control tool built on top of
+[ADAM](https://github.com/bigdatagenomics/adam). These containers build
+the Quinine codebase from HEAD, and then run the quinine-submit scripts that submit
+the code/command to a running Spark cluster.
+
+Running
+===
+
+When the runtime container is run, a port should be opened for the ADAM driver
+to communicate with the [Spark master](../apache-spark-master/README.md). The
+number of this port should be passed to Quinine as the Spark option
+`--conf spark.driver.port <portnumber>`. If run without additional configuration
+flags, Quinine will run in [Spark's local
+mode](http://spark.apache.org/docs/latest/#running-the-examples-and-shell).
+
+An example command is:
+
+```
+docker run \
+ --net=host \
+ -p 9999:9999 \
+ quay.io/ucsc_cgl/adam:latest \
+ --master spark://<spark_master_ip>:7077 \
+ --conf spark.driver.port=9999 -- \
+ flagstat hdfs://<hdfs_master_ip>:8020/mouse_chrM.bam 
+```
+

quinine/build/Dockerfile

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+FROM quay.io/ucsc_cgl/spark-and-maven:1.5.2.3.3.9
+
+MAINTAINER Frank Austin Nothaft, [email protected]
+
+WORKDIR /home
+
+# clone adam
+RUN git clone https:/bigdatagenomics/quinine.git
+
+# build adam
+WORKDIR /home/quinine
+RUN git checkout 3e5f19bf1399e1447a42a2359c01be54d75b183d
+
+RUN /opt/apache-maven-3.3.9/bin/mvn package -DskipTests

quinine/runtime/.gitignore

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+quinine

quinine/runtime/Dockerfile

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+FROM quay.io/ucsc_cgl/adam:962-ehf--be13567d00cd4c586edf8ae47d991815c8c72a49
+
+MAINTAINER Frank Austin Nothaft, [email protected]
+
+# copy jar
+COPY quinine /opt/cgl-docker-lib/quinine
+
+ENTRYPOINT ["/opt/cgl-docker-lib/quinine/bin/quinine-submit"]