Issues/263 create rtgtools image (#264)

* issues/223 - first pass at rtg_tools image

* fixed unit test

* adding command to install tabix (useful for vcfeval work)

* rtg-tools fix post code review

Author: tpesout

.gitignore

@@ -4,3 +4,4 @@
 *#*
 *.idea
 
+rtg_tools/runtime/LICENSE.txt

rtg_tools/Makefile

@@ -0,0 +1,33 @@
+# Definitions
+build_output = runtime/rtg-tools.jar
+runtime_fullpath = $(realpath runtime)
+build_tool = runtime-container.DONE
+git_commit ?= $(shell git log --pretty=oneline -n 1 -- ../rtg_tools | cut -f1 -d " ")
+name = quay.io/ucsc_cgl/rtg_tools
+tag = 3.8.3--${git_commit}
+
+# Steps
+build: ${build_output} ${build_tool}
+
+${build_output}: build/Dockerfile
+	cd build && docker build -t rtgtoolsbuild .
+	docker run -v ${runtime_fullpath}:/data rtgtoolsbuild cp /home/rtgtools-protected/rtg-tools.jar /home/rtgtools-protected/LICENSE.txt /data
+
+${build_tool}: ${build_output} runtime/Dockerfile
+	cd runtime && docker build -t ${name}:${tag} .
+	-docker rmi ${name}:latest
+	docker tag ${name}:${tag} ${name}:latest
+	-docker rmi -f rtgtoolsbuild
+	touch ${build_tool}
+
+push: build
+	# Requires ~/.dockercfg
+	docker push ${name}:${tag}
+	docker push ${name}:latest
+
+test: build
+	python test.py
+
+clean:
+	-rm ${build_tool}
+	-rm ${build_output}

rtg_tools/build/Dockerfile

@@ -0,0 +1,25 @@
+FROM java:8-jdk
+
+MAINTAINER Trevor Pesout, [email protected]
+
+RUN apt-get update && apt-get install -y \
+    git \
+	ant \
+	unzip
+
+# Create a new source directory
+WORKDIR /home
+
+# Get RTG tools
+WORKDIR /home/rtg-tools
+RUN git clone https://github.com/RealTimeGenomics/rtg-tools.git
+WORKDIR /home/rtg-tools/rtg-tools
+RUN git checkout 3.8.3
+
+# build
+RUN ant zip-nojre
+
+# Move jar to currently mounted directory (file is used in the runtime image)
+WORKDIR /home/rtgtools-protected
+RUN mv /home/rtg-tools/rtg-tools/build/rtg-tools.jar /home/rtgtools-protected/rtg-tools.jar
+RUN mv /home/rtg-tools/rtg-tools/LICENSE.txt /home/rtgtools-protected/LICENSE.txt

rtg_tools/runtime/Dockerfile

@@ -0,0 +1,16 @@
+FROM java:8-jdk
+MAINTAINER Trevor Pesout, [email protected]
+
+RUN apt-get update && apt-get install -y tabix
+
+# Copy over jar and place in /opt/cgl-docker-lib
+RUN mkdir /opt/rtg_tools
+COPY rtg-tools.jar  /opt/rtg_tools/
+COPY LICENSE.txt /opt/rtg_tools/
+COPY wrapper.sh /opt/rtg_tools/
+
+# Set WORKDIR to /data -- predefined mount location.
+RUN mkdir /data
+WORKDIR /data
+
+ENTRYPOINT ["sh", "/opt/rtg_tools/wrapper.sh"]

rtg_tools/runtime/wrapper.sh

@@ -0,0 +1,14 @@
+#!/usr/bin/env bash
+set -e
+
+# Fix ownership of output files
+finish() {
+    # Fix ownership of output files
+    user_id=$(stat -c '%u:%g' /data)
+    chown -R ${user_id} /data
+}
+trap finish EXIT
+
+# Call tool with parameters
+java $JAVA_OPTS -jar /opt/rtg_tools/rtg-tools.jar "$@"
+

rtg_tools/test.py

@@ -0,0 +1,21 @@
+#!/usr/bin/env python2.7
+# Trevor Pesout
+import subprocess
+import tempfile
+import unittest
+
+
+class TestRTGTools(unittest.TestCase):
+
+    def test_docker_call(self):
+        out, err = check_docker_output(tool='quay.io/ucsc_cgl/rtg_tools')
+        self.assertTrue('RTG Tools 3.8.3' in out)
+
+def check_docker_output(tool):
+    command = 'docker run --rm {} version'.format(tool)
+    process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+    output = process.communicate()
+    return output
+
+if __name__ == '__main__':
+    unittest.main()