Small changes to polisher Dockerfile and runModelPolisher script. Hop…

…efully fixed the lockup when running non-root container

docker/java_docker/Dockerfile

@@ -1,6 +1,6 @@
 FROM openjdk:11-slim
 MAINTAINER zajac.thomas1992@gmail.com
 
-RUN mkdir .java
+RUN mkdir -p /.java/.systemPrefs && mkdir /.java/.userPrefs && chmod -R 755 /.java
 COPY ModelPolisher-2.1-beta.jar /
 CMD "/bin/sh"

runModelPolisher.sh

@@ -4,4 +4,4 @@ if [ ! -x "$(command -v docker)" ]; then echo "Docker is not installed, please s
 MODELS=$1
 if [ -z ${MODELS} ]; then echo "Path to model folder is either empty or not set. Please set correct path"; exit -2; fi
 if [ ! -d ${MODELS} ]; then echo "Path does not point to directory: ${MODELS}"; exit -3; fi
-docker-compose run -u $(id -u):$(id -g) -v ${MODELS}:/models polisher java -Djava.util.prefs.userRoot=/ -jar /ModelPolisher-2.1-beta.jar --input=/models/ --output=/models/out --annotate-with-bigg=true --sbml-validation=true --compression-type=GZIP
+docker-compose run -u $(id -u):$(id -g) -v ${MODELS}:/models polisher java -Djava.util.prefs.userRoot=/.java -jar /ModelPolisher-2.1-beta.jar --input=/models/ --output=/models/out --annotate-with-bigg=true --sbml-validation=true --compression-type=GZIP