Dockerfile

FROM ubuntu:trusty

MAINTAINER Kristian Peters <kpeters@ipb-halle.de>

LABEL Description="Install nmrML in Docker."

# Update & upgrade sources
RUN apt-get -y update
RUN apt-get -y dist-upgrade

# Install mandatory packages
RUN apt-get -y install build-essential software-properties-common
RUN apt-get install -y byobu curl git htop man unzip vim wget

# Install Java
RUN echo oracle-java7-installer shared/accepted-oracle-license-v1-1 select true | debconf-set-selections
#RUN add-apt-repository -y ppa:webupd8team/java
#RUN apt-get -y update
#RUN apt-get -y install oracle-java7-installer
RUN apt-get -y install openjdk-7-jdk openjdk-7-jre

# Clean up
RUN apt-get -y clean && apt-get -y autoremove && rm -rf /var/lib/{cache,log}/ /var/cache/oracle-jdk7-installer /tmp/* /var/tmp/*

# Clone nmrML github repo
WORKDIR /usr/src
RUN git clone https://github.com/nmrML/nmrML

# Install nmrML converter
WORKDIR /usr/src/nmrML/tools/Parser_and_Converters/Java/converter
RUN install -m755 bin/nmrMLcreate /usr/local/bin
RUN install -m755 bin/nmrMLproc /usr/local/bin
ADD nmrMLconv.sh /usr/local/bin/nmrMLconv
RUN mkdir /usr/local/share/nmrML
RUN install -m755 bin/converter.jar /usr/local/share/nmrML/

# Set JAVA_HOME
#ENV JAVA_HOME /usr/lib/jvm/java-7-oracle
#ENV JAVA_HOME /usr/lib/jvm/default-java

# Define data directory
RUN mkdir /data
WORKDIR /data

ENTRYPOINT ["sh","/usr/local/bin/nmrMLconv"]