Provided a helper script for passing JVM args to docker.

Also added a docker ignore

.dockerignore

@@ -0,0 +1,18 @@
+.git
+.gitignore
+.jar_opt
+.classpath
+.project
+.travis.yml
+build.sbt
+Picard-public.fbp
+Picard-public.iml
+Picard-public.ipr
+README.md
+classes
+dist
+etc
+htsjdk
+project
+testclasses
+testdata

Dockerfile

@@ -19,6 +19,13 @@ WORKDIR /usr/picard
 RUN git config --global http.sslVerify false && git clone https://github.com/samtools/htsjdk.git
 
 # Build the distribution jar, clean up everything else
-RUN ant clean all && mv dist/picard.jar picard.jar && ant clean && rm -rf htsjdk && rm -rf src && rm -rf lib && rm build.xml
+RUN ant clean all && \
+    mv dist/picard.jar picard.jar && \
+    mv src/scripts/picard/docker_helper.sh docker_helper.sh && \
+    ant clean && \
+    rm -rf htsjdk && \
+    rm -rf src && \
+    rm -rf lib && \
+    rm build.xml
 
-ENTRYPOINT ["java", "-jar", "picard.jar"]
+ENTRYPOINT ["./docker_helper.sh"]

src/scripts/picard/docker_helper.sh

@@ -0,0 +1,27 @@
+#!/usr/bin/env bash
+
+# Example Usage: ./docker_helper.sh -j "-XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xmx4000m" MarkDuplicates INPUT=fake.bam ...
+usage() {
+  cat << EOF
+Usage: $0 [-j <JVM arguments>] tool_name tool_arguments
+
+Run Picard with JVM args and program args if present. Assumes picard.jar lives in the same directory.
+JVM arguments should be a quoted, space separated list.
+
+Example Usage:
+./docker_helper.sh -j "-XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xmx4000m" MarkDuplicates INPUT=fake.bam ...
+
+EOF
+  exit 1
+}
+while getopts "j:h" OPTION; do
+  case $OPTION in
+    j) JVM_ARGS=$OPTARG;;
+    h) usage; exit 0;;
+    [?]) usage; exit 1;;
+  esac
+done
+shift $(expr $OPTIND - 1)
+TOOL_WITH_ARGS=$@
+
+java ${JVM_ARGS} -jar picard.jar ${TOOL_WITH_ARGS}